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Database: PDB
Entry: 6ETE
LinkDB: 6ETE
Original site: 6ETE 
HEADER    OXIDOREDUCTASE                          26-OCT-17   6ETE              
TITLE     CRYSTAL STRUCTURE OF KDM4D WITH TETRAZOLHYDRAZIDE COMPOUND 5          
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D;                            
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: JMJD2D;                                                    
COMPND   5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D,    
COMPND   6 JUMONJI DOMAIN-CONTAINING PROTEIN 2D;                                
COMPND   7 EC: 1.14.11.-;                                                       
COMPND   8 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: KDM4D, JHDM3D, JMJD2D;                                         
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);                       
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID                               
KEYWDS    KDM4D, LIGAND BINDING, TETRAZOLYLHYDRAZIDE, TETRAZOLE, INHIBITOR      
KEYWDS   2 DESIGN, CANCER, EPIGENETICS, OXIDOREDUCTASE                          
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    P.H.MALECKI,M.S.WEISS,U.HEINEMANN,A.LINK                              
REVDAT   1   20-FEB-19 6ETE    0                                                
JRNL        AUTH   P.H.MALECKI,A.LINK,M.S.WEISS,U.HEINEMANN                     
JRNL        TITL   CRYSTAL STRUCTURE OF KDM4D WITH TETRAZOLYLHYDRAZIDE LIGAND   
JRNL        TITL 2 NR128                                                        
JRNL        REF    TO BE PUBLISHED                                              
JRNL        REFN                                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.47 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX                                               
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : ML                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 35.73                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.330                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.8                           
REMARK   3   NUMBER OF REFLECTIONS             : 127487                         
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.128                           
REMARK   3   R VALUE            (WORKING SET) : 0.128                           
REMARK   3   FREE R VALUE                     : 0.153                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 1.630                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 2081                            
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
REMARK   3     1 35.7426 -  3.6190    1.00     8366   132  0.1327 0.1706        
REMARK   3     2  3.6190 -  2.8729    1.00     8364   142  0.1246 0.1251        
REMARK   3     3  2.8729 -  2.5098    1.00     8370   134  0.1218 0.1350        
REMARK   3     4  2.5098 -  2.2804    1.00     8361   138  0.1165 0.1386        
REMARK   3     5  2.2804 -  2.1170    1.00     8382   139  0.1075 0.1598        
REMARK   3     6  2.1170 -  1.9922    1.00     8375   141  0.1083 0.1177        
REMARK   3     7  1.9922 -  1.8924    1.00     8365   143  0.1073 0.1619        
REMARK   3     8  1.8924 -  1.8100    1.00     8409   141  0.1128 0.1347        
REMARK   3     9  1.8100 -  1.7404    1.00     8283   139  0.1262 0.1670        
REMARK   3    10  1.7404 -  1.6803    1.00     8400   143  0.1353 0.1718        
REMARK   3    11  1.6803 -  1.6278    1.00     8332   136  0.1461 0.1669        
REMARK   3    12  1.6278 -  1.5812    1.00     8409   139  0.1579 0.2104        
REMARK   3    13  1.5812 -  1.5396    1.00     8358   141  0.1777 0.2146        
REMARK   3    14  1.5396 -  1.5021    1.00     8425   136  0.1973 0.2113        
REMARK   3    15  1.5021 -  1.4679    0.98     8207   137  0.2254 0.2668        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
REMARK   3   SOLVENT RADIUS     : 1.11                                          
REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
REMARK   3   K_SOL              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.130            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.980           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 18.05                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 27.33                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  TWINNING INFORMATION.                                               
REMARK   3   FRACTION: NULL                                                     
REMARK   3   OPERATOR: NULL                                                     
REMARK   3                                                                      
REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
REMARK   3                 RMSD          COUNT                                  
REMARK   3   BOND      :  0.031           3074                                  
REMARK   3   ANGLE     :  2.362           4205                                  
REMARK   3   CHIRALITY :  0.166            421                                  
REMARK   3   PLANARITY :  0.016            558                                  
REMARK   3   DIHEDRAL  : 15.719           1182                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  NCS DETAILS                                                         
REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 6ETE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-OCT-17.                  
REMARK 100 THE DEPOSITION ID IS D_1200007227.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 04-MAY-16                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7                                  
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : BESSY                              
REMARK 200  BEAMLINE                       : 14.1                               
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.918                              
REMARK 200  MONOCHROMATOR                  : DOUBLE CRYSTAL                     
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS 6M                 
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : XSCALE                             
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 127491                             
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.470                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 47.923                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.8                               
REMARK 200  DATA REDUNDANCY                : 4.607                              
REMARK 200  R MERGE                    (I) : 0.04400                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 18.1600                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.56                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 99.3                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.54                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.69400                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 2.020                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: REFMAC                                                
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 51.42                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES, 180MM AMMONIUM SULPHATE,    
REMARK 280  24% PEG 3350, PH 7, VAPOR DIFFUSION, TEMPERATURE 293K               
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2                        
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,-Y,Z+1/2                                             
REMARK 290       3555   -Y+1/2,X+1/2,Z+3/4                                      
REMARK 290       4555   Y+1/2,-X+1/2,Z+1/4                                      
REMARK 290       5555   -X+1/2,Y+1/2,-Z+3/4                                     
REMARK 290       6555   X+1/2,-Y+1/2,-Z+1/4                                     
REMARK 290       7555   Y,X,-Z                                                  
REMARK 290       8555   -Y,-X,-Z+1/2                                            
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       75.53500            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       35.73200            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       35.73200            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000      113.30250            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       35.73200            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       35.73200            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       37.76750            
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       35.73200            
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       35.73200            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000      113.30250            
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       35.73200            
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       35.73200            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       37.76750            
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       75.53500            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 2100 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 14950 ANGSTROM**2                       
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL                        
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     MET A     1                                                      
REMARK 465     GLU A     2                                                      
REMARK 465     THR A     3                                                      
REMARK 465     MET A     4                                                      
REMARK 465     LYS A     5                                                      
REMARK 465     SER A     6                                                      
REMARK 465     LYS A     7                                                      
REMARK 465     ALA A     8                                                      
REMARK 465     ASN A     9                                                      
REMARK 465     CYS A    10                                                      
REMARK 465     ASP A   341                                                      
REMARK 465     ARG A   342                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS                                      
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)               
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   RES CSSEQI ATM2   DEVIATION                     
REMARK 500    ARG A 228   N     ARG A 228   CA      0.135                       
REMARK 500    MET A 321   N     MET A 321   CA      0.185                       
REMARK 500    GLU A 331   N     GLU A 331   CA      0.121                       
REMARK 500    ASP A 334   CA    ASP A 334   C       0.162                       
REMARK 500    ASP A 334   CA    ASP A 334   C       0.162                       
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500    ARG A 102   NE  -  CZ  -  NH1 ANGL. DEV. =   4.1 DEGREES          
REMARK 500    ARG A 102   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.0 DEGREES          
REMARK 500    ILE A 160   CB  -  CA  -  C   ANGL. DEV. = -15.4 DEGREES          
REMARK 500    MET A 196   CG  -  SD  -  CE  ANGL. DEV. =  13.0 DEGREES          
REMARK 500    MET A 321   CG  -  SD  -  CE  ANGL. DEV. =  13.0 DEGREES          
REMARK 500    ASP A 322   CB  -  CG  -  OD1 ANGL. DEV. =   7.5 DEGREES          
REMARK 500    ASP A 322   CB  -  CG  -  OD2 ANGL. DEV. =  -6.1 DEGREES          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: TORSION ANGLES                                             
REMARK 500                                                                      
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:            
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                    
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-           
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400            
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        PSI       PHI                                   
REMARK 500    LYS A 186       -7.75     75.61                                   
REMARK 500    MET A 196       19.92     50.89                                   
REMARK 500    MET A 196       21.15     49.80                                   
REMARK 500    ASP A 334      -58.54    -29.89                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 525                                                                      
REMARK 525 SOLVENT                                                              
REMARK 525                                                                      
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT                    
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST                  
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT                 
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE                       
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;                             
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE                  
REMARK 525 NUMBER; I=INSERTION CODE):                                           
REMARK 525                                                                      
REMARK 525  M RES CSSEQI                                                        
REMARK 525    HOH A 850        DISTANCE =  5.87 ANGSTROMS                       
REMARK 525    HOH A 851        DISTANCE =  8.44 ANGSTROMS                       
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              NI A 403  NI                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 HIS A 156   NE2                                                    
REMARK 620 2 HOH A 721   O    83.1                                              
REMARK 620 N                    1                                               
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              NI A 402  NI                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 HIS A 192   NE2                                                    
REMARK 620 2 GLU A 194   OE2  98.9                                              
REMARK 620 3 HIS A 280   NE2  85.9  86.7                                        
REMARK 620 4 BWK A 413   O    89.5 171.5  92.8                                  
REMARK 620 5 BWK A 413   N4  142.3 118.7  98.5  53.0                            
REMARK 620 6 BWK A 413   N5  168.3  92.2  98.4  79.5  26.5                      
REMARK 620 7 HOH A 569   O    87.9  91.2 173.1  90.3  88.2  88.2                
REMARK 620 N                    1     2     3     4     5     6                 
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN A 401  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 238   SG                                                     
REMARK 620 2 HIS A 244   NE2 107.7                                              
REMARK 620 3 CYS A 310   SG  116.1 109.7                                        
REMARK 620 4 CYS A 312   SG  114.5 101.5 106.3                                  
REMARK 620 N                    1     2     3                                   
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 402                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 403                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC4                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC5                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC6                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC7                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC8                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC9                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AD1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AD2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 411                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AD3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 412                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AD4                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue BWK A 413                 
DBREF  6ETE A    1   342  UNP    Q6B0I6   KDM4D_HUMAN      1    342             
SEQRES   1 A  342  MET GLU THR MET LYS SER LYS ALA ASN CYS ALA GLN ASN          
SEQRES   2 A  342  PRO ASN CYS ASN ILE MET ILE PHE HIS PRO THR LYS GLU          
SEQRES   3 A  342  GLU PHE ASN ASP PHE ASP LYS TYR ILE ALA TYR MET GLU          
SEQRES   4 A  342  SER GLN GLY ALA HIS ARG ALA GLY LEU ALA LYS ILE ILE          
SEQRES   5 A  342  PRO PRO LYS GLU TRP LYS ALA ARG GLU THR TYR ASP ASN          
SEQRES   6 A  342  ILE SER GLU ILE LEU ILE ALA THR PRO LEU GLN GLN VAL          
SEQRES   7 A  342  ALA SER GLY ARG ALA GLY VAL PHE THR GLN TYR HIS LYS          
SEQRES   8 A  342  LYS LYS LYS ALA MET THR VAL GLY GLU TYR ARG HIS LEU          
SEQRES   9 A  342  ALA ASN SER LYS LYS TYR GLN THR PRO PRO HIS GLN ASN          
SEQRES  10 A  342  PHE GLU ASP LEU GLU ARG LYS TYR TRP LYS ASN ARG ILE          
SEQRES  11 A  342  TYR ASN SER PRO ILE TYR GLY ALA ASP ILE SER GLY SER          
SEQRES  12 A  342  LEU PHE ASP GLU ASN THR LYS GLN TRP ASN LEU GLY HIS          
SEQRES  13 A  342  LEU GLY THR ILE GLN ASP LEU LEU GLU LYS GLU CYS GLY          
SEQRES  14 A  342  VAL VAL ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE          
SEQRES  15 A  342  GLY MET TRP LYS THR THR PHE ALA TRP HIS THR GLU ASP          
SEQRES  16 A  342  MET ASP LEU TYR SER ILE ASN TYR LEU HIS LEU GLY GLU          
SEQRES  17 A  342  PRO LYS THR TRP TYR VAL VAL PRO PRO GLU HIS GLY GLN          
SEQRES  18 A  342  ARG LEU GLU ARG LEU ALA ARG GLU LEU PHE PRO GLY SER          
SEQRES  19 A  342  SER ARG GLY CYS GLY ALA PHE LEU ARG HIS LYS VAL ALA          
SEQRES  20 A  342  LEU ILE SER PRO THR VAL LEU LYS GLU ASN GLY ILE PRO          
SEQRES  21 A  342  PHE ASN ARG ILE THR GLN GLU ALA GLY GLU PHE MET VAL          
SEQRES  22 A  342  THR PHE PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY          
SEQRES  23 A  342  PHE ASN CYS ALA GLU ALA ILE ASN PHE ALA THR PRO ARG          
SEQRES  24 A  342  TRP ILE ASP TYR GLY LYS MET ALA SER GLN CYS SER CYS          
SEQRES  25 A  342  GLY GLU ALA ARG VAL THR PHE SER MET ASP ALA PHE VAL          
SEQRES  26 A  342  ARG ILE LEU GLN PRO GLU ARG TYR ASP LEU TRP LYS ARG          
SEQRES  27 A  342  GLY GLN ASP ARG                                              
HET     ZN  A 401       1                                                       
HET     NI  A 402       1                                                       
HET     NI  A 403       1                                                       
HET    EDO  A 404      10                                                       
HET    EDO  A 405      10                                                       
HET    EDO  A 406      10                                                       
HET    EDO  A 407      10                                                       
HET    EDO  A 408      10                                                       
HET    EDO  A 409      10                                                       
HET    EDO  A 410      10                                                       
HET    SO4  A 411       5                                                       
HET    SO4  A 412       5                                                       
HET    BWK  A 413      21                                                       
HETNAM      ZN ZINC ION                                                         
HETNAM      NI NICKEL (II) ION                                                  
HETNAM     EDO 1,2-ETHANEDIOL                                                   
HETNAM     SO4 SULFATE ION                                                      
HETNAM     BWK [2-(1-METHYL-1,2,3,4-TETRAZOL-4-IUM-5-YL)                        
HETNAM   2 BWK  ETHANOYLAMINO]AZANIUM                                           
HETSYN     EDO ETHYLENE GLYCOL                                                  
FORMUL   2   ZN    ZN 2+                                                        
FORMUL   3   NI    2(NI 2+)                                                     
FORMUL   5  EDO    7(C2 H6 O2)                                                  
FORMUL  12  SO4    2(O4 S 2-)                                                   
FORMUL  14  BWK    C4 H10 N6 O 2+                                               
FORMUL  15  HOH   *351(H2 O)                                                    
HELIX    1 AA1 ASP A   30  GLN A   41  1                                  12    
HELIX    2 AA2 GLY A   42  ALA A   46  5                                   5    
HELIX    3 AA3 VAL A   98  ASN A  106  1                                   9    
HELIX    4 AA4 ASN A  117  ARG A  129  1                                  13    
HELIX    5 AA5 ILE A  130  ASN A  132  5                                   3    
HELIX    6 AA6 THR A  159  GLY A  169  1                                  11    
HELIX    7 AA7 GLU A  194  LEU A  198  5                                   5    
HELIX    8 AA8 PRO A  216  GLU A  218  5                                   3    
HELIX    9 AA9 HIS A  219  PHE A  231  1                                  13    
HELIX   10 AB1 PHE A  231  CYS A  238  1                                   8    
HELIX   11 AB2 ALA A  240  LYS A  245  5                                   6    
HELIX   12 AB3 SER A  250  ASN A  257  1                                   8    
HELIX   13 AB4 ARG A  299  ALA A  307  1                                   9    
HELIX   14 AB5 THR A  318  GLN A  329  1                                  12    
HELIX   15 AB6 GLN A  329  GLN A  340  1                                  12    
SHEET    1 AA110 MET A  19  PHE A  21  0                                        
SHEET    2 AA110 LEU A  48  ILE A  51  1  O  LYS A  50   N  PHE A  21           
SHEET    3 AA110 PHE A 271  THR A 274 -1  O  PHE A 271   N  ILE A  51           
SHEET    4 AA110 TYR A 199  GLY A 207 -1  N  ASN A 202   O  MET A 272           
SHEET    5 AA110 ASN A 288  PHE A 295 -1  O  GLU A 291   N  TYR A 203           
SHEET    6 AA110 TYR A 179  GLY A 183 -1  N  TYR A 181   O  ALA A 290           
SHEET    7 AA110 ILE A 135  SER A 141 -1  N  GLY A 137   O  PHE A 182           
SHEET    8 AA110 LEU A  75  ARG A  82 -1  N  LEU A  75   O  TYR A 136           
SHEET    9 AA110 VAL A  85  LYS A  92 -1  O  LYS A  91   N  GLN A  76           
SHEET   10 AA110 ALA A 247  ILE A 249 -1  O  LEU A 248   N  PHE A  86           
SHEET    1 AA2 2 LEU A  70  ILE A  71  0                                        
SHEET    2 AA2 2 MET A  96  THR A  97 -1  O  MET A  96   N  ILE A  71           
SHEET    1 AA3 4 THR A 188  HIS A 192  0                                        
SHEET    2 AA3 4 TYR A 279  ASN A 284 -1  O  GLY A 282   N  PHE A 189           
SHEET    3 AA3 4 LYS A 210  VAL A 215 -1  N  TYR A 213   O  ALA A 281           
SHEET    4 AA3 4 ASN A 262  GLN A 266 -1  O  ILE A 264   N  TRP A 212           
LINK         NE2 HIS A 156                NI    NI A 403     1555   1555  2.18  
LINK         NE2 HIS A 192                NI    NI A 402     1555   1555  2.12  
LINK         OE2 GLU A 194                NI    NI A 402     1555   1555  2.04  
LINK         SG  CYS A 238                ZN    ZN A 401     1555   1555  2.30  
LINK         NE2 HIS A 244                ZN    ZN A 401     1555   1555  2.10  
LINK         NE2 HIS A 280                NI    NI A 402     1555   1555  2.11  
LINK         SG  CYS A 310                ZN    ZN A 401     1555   1555  2.29  
LINK         SG  CYS A 312                ZN    ZN A 401     1555   1555  2.31  
LINK        NI    NI A 402                 O  BBWK A 413     1555   1555  2.08  
LINK        NI    NI A 402                 N4 BBWK A 413     1555   1555  2.63  
LINK        NI    NI A 402                 N5 BBWK A 413     1555   1555  1.76  
LINK        NI    NI A 402                 O   HOH A 569     1555   1555  2.12  
LINK        NI    NI A 403                 O   HOH A 721     1555   1555  2.33  
SITE     1 AC1  4 CYS A 238  HIS A 244  CYS A 310  CYS A 312                    
SITE     1 AC2  5 HIS A 192  GLU A 194  HIS A 280  BWK A 413                    
SITE     2 AC2  5 HOH A 569                                                     
SITE     1 AC3  2 HIS A 156  HOH A 721                                          
SITE     1 AC4  4 ARG A 123  LYS A 124  LYS A 127  ASN A 128                    
SITE     1 AC5  8 LYS A 150  GLN A 151  TRP A 152  ASN A 153                    
SITE     2 AC5  8 HIS A 156  LEU A 157  HOH A 550  HOH A 704                    
SITE     1 AC6  3 LYS A 255  ARG A 263  HOH A 539                               
SITE     1 AC7  5 PHE A 118  ARG A 263  ILE A 264  THR A 265                    
SITE     2 AC7  5 HOH A 542                                                     
SITE     1 AC8  7 LYS A 109  GLN A 111  ASN A 132  TRP A 185                    
SITE     2 AC8  7 LYS A 186  SO4 A 411  HOH A 511                               
SITE     1 AC9  4 HIS A 103  ASN A 106  HOH A 518  HOH A 624                    
SITE     1 AD1  8 TYR A 179  TYR A 181  GLU A 194  SER A 200                    
SITE     2 AD1  8 ALA A 292  ASN A 294  BWK A 413  HOH A 569                    
SITE     1 AD2  6 PRO A 113  LYS A 124  ASN A 128  TRP A 185                    
SITE     2 AD2  6 LYS A 186  EDO A 408                                          
SITE     1 AD3  6 ARG A  60  GLU A  61  THR A  62  HOH A 503                    
SITE     2 AD3  6 HOH A 523  HOH A 851                                          
SITE     1 AD4 13 TYR A 181  HIS A 192  GLU A 194  SER A 200                    
SITE     2 AD4 13 ASN A 202  LYS A 210  TRP A 212  HIS A 280                    
SITE     3 AD4 13 ALA A 292   NI A 402  EDO A 410  HOH A 569                    
SITE     4 AD4 13 HOH A 580                                                     
CRYST1   71.464   71.464  151.070  90.00  90.00  90.00 P 43 21 2     8          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.013993  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.013993  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.006619        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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