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Database: PDB
Entry: 5YDR
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Original site: 5YDR 
HEADER    PROTEIN BINDING/TRANSFERASE             14-SEP-17   5YDR              
TITLE     STRUCTURE OF DNMT1 RFTS DOMAIN IN COMPLEX WITH UBIQUITIN              
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: POLYUBIQUITIN-B;                                           
COMPND   3 CHAIN: A, D;                                                         
COMPND   4 FRAGMENT: UNP RESIDUES 1-73;                                         
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 MOL_ID: 2;                                                           
COMPND   7 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 1;                      
COMPND   8 CHAIN: B;                                                            
COMPND   9 FRAGMENT: RFTS DOMAIN, UNP RESIDUES 351-599;                         
COMPND  10 SYNONYM: DNMT1,CXXC-TYPE ZINC FINGER PROTEIN 9,DNA METHYLTRANSFERASE 
COMPND  11 HSAI,M.HSAI,MCMT;                                                    
COMPND  12 EC: 2.1.1.37;                                                        
COMPND  13 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: UBB;                                                           
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 MOL_ID: 2;                                                           
SOURCE   9 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE  10 ORGANISM_COMMON: HUMAN;                                              
SOURCE  11 ORGANISM_TAXID: 9606;                                                
SOURCE  12 GENE: DNMT1, AIM, CXXC9, DNMT;                                       
SOURCE  13 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE  14 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    DNA METHYLATION, PROTEIN BINDING, PROTEIN BINDING-TRANSFERASE COMPLEX 
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    C.QIAN                                                                
REVDAT   2   18-APR-18 5YDR    1       JRNL                                     
REVDAT   1   21-FEB-18 5YDR    0                                                
JRNL        AUTH   T.LI,L.WANG,Y.DU,S.XIE,X.YANG,F.LIAN,Z.ZHOU,C.QIAN           
JRNL        TITL   STRUCTURAL AND MECHANISTIC INSIGHTS INTO UHRF1-MEDIATED      
JRNL        TITL 2 DNMT1 ACTIVATION IN THE MAINTENANCE DNA METHYLATION.         
JRNL        REF    NUCLEIC ACIDS RES.            V.  46  3218 2018              
JRNL        REFN                   ESSN 1362-4962                               
JRNL        PMID   29471350                                                     
JRNL        DOI    10.1093/NAR/GKY104                                           
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.00 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX DEV_2067                                      
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 : NULL                                          
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 44.77                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.340                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.2                           
REMARK   3   NUMBER OF REFLECTIONS             : 79112                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.200                           
REMARK   3   R VALUE            (WORKING SET) : 0.199                           
REMARK   3   FREE R VALUE                     : 0.233                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.900                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 3874                            
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 44.7804 -  6.0779    0.99     2724    88  0.1690 0.1525        
REMARK   3     2  6.0779 -  4.8260    1.00     2718   142  0.1759 0.2098        
REMARK   3     3  4.8260 -  4.2165    1.00     2714   144  0.1440 0.1588        
REMARK   3     4  4.2165 -  3.8312    1.00     2681   145  0.1619 0.2628        
REMARK   3     5  3.8312 -  3.5567    0.99     2703   134  0.1832 0.2110        
REMARK   3     6  3.5567 -  3.3471    1.00     2727   124  0.2011 0.2622        
REMARK   3     7  3.3471 -  3.1795    1.00     2685   144  0.2122 0.2310        
REMARK   3     8  3.1795 -  3.0411    1.00     2704   129  0.2293 0.2716        
REMARK   3     9  3.0411 -  2.9241    1.00     2687   180  0.2297 0.2586        
REMARK   3    10  2.9241 -  2.8232    1.00     2666   166  0.2296 0.2593        
REMARK   3    11  2.8232 -  2.7349    0.99     2682   137  0.2285 0.2321        
REMARK   3    12  2.7349 -  2.6568    1.00     2720   136  0.2231 0.2364        
REMARK   3    13  2.6568 -  2.5868    0.99     2637   152  0.2150 0.2399        
REMARK   3    14  2.5868 -  2.5237    0.99     2719   118  0.2286 0.2592        
REMARK   3    15  2.5237 -  2.4664    1.00     2700   158  0.2273 0.2641        
REMARK   3    16  2.4664 -  2.4139    0.99     2714    84  0.2273 0.3014        
REMARK   3    17  2.4139 -  2.3656    1.00     2713   144  0.2186 0.2508        
REMARK   3    18  2.3656 -  2.3210    0.98     2736   110  0.2270 0.2891        
REMARK   3    19  2.3210 -  2.2795    1.00     2611   168  0.2177 0.2606        
REMARK   3    20  2.2795 -  2.2409    0.98     2621   176  0.2194 0.2571        
REMARK   3    21  2.2409 -  2.2047    1.00     2683   144  0.2247 0.2268        
REMARK   3    22  2.2047 -  2.1708    0.99     2669   136  0.2089 0.2600        
REMARK   3    23  2.1708 -  2.1389    0.98     2688   101  0.2184 0.2649        
REMARK   3    24  2.1389 -  2.1088    1.00     2667   171  0.2213 0.2257        
REMARK   3    25  2.1088 -  2.0803    0.97     2666   138  0.2284 0.2363        
REMARK   3    26  2.0803 -  2.0532    1.00     2705   110  0.2372 0.2754        
REMARK   3    27  2.0532 -  2.0276    0.99     2662   143  0.2552 0.2955        
REMARK   3    28  2.0276 -  2.0032    0.97     2636   152  0.2549 0.3293        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : NULL                                          
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)     : 0.220            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.180           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 44.02                          
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      :  0.009           3165                                  
REMARK   3   ANGLE     :  1.415           4296                                  
REMARK   3   CHIRALITY :  0.062            487                                  
REMARK   3   PLANARITY :  0.010            562                                  
REMARK   3   DIHEDRAL  : 10.471           3064                                  
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: THE STRUCTURE FACTOR FILE CONTAINS        
REMARK   3  FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS                               
REMARK   4                                                                      
REMARK   4 5YDR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-SEP-17.                  
REMARK 100 THE DEPOSITION ID IS D_1300005100.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 21-DEC-14                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 8.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SSRF                               
REMARK 200  BEAMLINE                       : BL17U1                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.979                              
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315R                  
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                           
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000                           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 79146                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.500                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.3                               
REMARK 200  DATA REDUNDANCY                : 10.80                              
REMARK 200  R MERGE                    (I) : 0.10500                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 5.7000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.47800                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHENIX                                                
REMARK 200 STARTING MODEL: 3AV4                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 63.81                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM TRIS-HCL, 200MM SODIUM ACETATE,     
REMARK 280  25% PEG 4000, PH 8.0, EVAPORATION, TEMPERATURE 291K                 
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65                             
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -Y,X-Y,Z+2/3                                            
REMARK 290       3555   -X+Y,-X,Z+1/3                                           
REMARK 290       4555   -X,-Y,Z+1/2                                             
REMARK 290       5555   Y,-X+Y,Z+1/6                                            
REMARK 290       6555   X-Y,X,Z+5/6                                             
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 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       40.68333            
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       20.34167            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       30.51250            
REMARK 290   SMTRY1   5  0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   5 -0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       10.17083            
REMARK 290   SMTRY1   6  0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   6  0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       50.85417            
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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC                          
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC                   
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 3560 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 19130 ANGSTROM**2                       
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL                        
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D                               
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     ALA D    -1                                                      
REMARK 465     LEU D    73                                                      
REMARK 470                                                                      
REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470     LYS A  48    CE   NZ                                             
REMARK 470     LYS A  63    CD   CE   NZ                                        
REMARK 470     LYS B 366    CD   CE   NZ                                        
REMARK 470     GLU B 393    CG   CD   OE1  OE2                                  
REMARK 470     GLU B 400    CG   CD   OE1  OE2                                  
REMARK 470     GLU B 494    CD   OE1  OE2                                       
REMARK 470     GLU B 525    CD   OE1  OE2                                       
REMARK 470     LYS B 586    CD   CE   NZ                                        
REMARK 470     HIS D   0    CG   ND1  CD2  CE1  NE2                             
REMARK 470     GLU D  16    CD   OE1  OE2                                       
REMARK 470     GLU D  24    CG   CD   OE1  OE2                                  
REMARK 470     ASN D  25    CG   OD1  ND2                                       
REMARK 470     LYS D  29    CE   NZ                                             
REMARK 470     THR D  55    CB   OG1  CG2                                       
REMARK 470     GLN D  62    OE1  NE2                                            
REMARK 470     LYS D  63    CG   CD   CE   NZ                                   
REMARK 470     ARG D  72    CG   CD   NE   CZ   NH1  NH2                        
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    PRO B 351   C   -  N   -  CA  ANGL. DEV. =  10.8 DEGREES          
REMARK 500    TYR B 413   CB  -  CG  -  CD2 ANGL. DEV. =  -9.3 DEGREES          
REMARK 500    TYR B 413   CB  -  CG  -  CD1 ANGL. DEV. =   4.0 DEGREES          
REMARK 500    PHE B 434   CB  -  CG  -  CD2 ANGL. DEV. =  -4.4 DEGREES          
REMARK 500    PHE B 435   CB  -  CG  -  CD2 ANGL. DEV. =  -9.4 DEGREES          
REMARK 500    PHE B 435   CB  -  CG  -  CD1 ANGL. DEV. =   5.5 DEGREES          
REMARK 500    TYR B 486   CB  -  CG  -  CD2 ANGL. DEV. =  -5.6 DEGREES          
REMARK 500    TYR B 507   CB  -  CG  -  CD2 ANGL. DEV. =  -6.0 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    GLU B 393        8.84    -69.62                                   
REMARK 500    PHE B 469       48.47    -92.23                                   
REMARK 500    MET B 489     -106.68   -109.37                                   
REMARK 500    ASP B 571       99.87    -52.80                                   
REMARK 500    ILE B 575      -63.59   -124.12                                   
REMARK 500    PHE B 576     -122.24     51.76                                   
REMARK 500    LEU B 577       58.65   -110.24                                   
REMARK 500    GLU D  64        4.75     56.77                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: PLANAR GROUPS                                              
REMARK 500                                                                      
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL                 
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE                    
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN                    
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS                        
REMARK 500 AN RMSD GREATER THAN THIS VALUE                                      
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        RMS     TYPE                                    
REMARK 500    TYR B 413         0.09    SIDE CHAIN                              
REMARK 500    PHE B 434         0.06    SIDE CHAIN                              
REMARK 500    PHE B 435         0.09    SIDE CHAIN                              
REMARK 500    TYR B 486         0.07    SIDE CHAIN                              
REMARK 500    TYR B 507         0.07    SIDE CHAIN                              
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 B 902        DISTANCE =  5.98 ANGSTROMS                       
REMARK 525    HOH B 903        DISTANCE =  6.44 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                              ZN B 601  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS B 353   SG                                                     
REMARK 620 2 CYS B 356   SG  106.2                                              
REMARK 620 3 CYS B 414   SG  118.7 122.2                                        
REMARK 620 4 HIS B 418   ND1 102.0 111.2  93.8                                  
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 PO4 A 101                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 601                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 602                 
DBREF  5YDR A    1    73  UNP    J3QS39   J3QS39_HUMAN     1     73             
DBREF  5YDR B  351   599  UNP    P26358   DNMT1_HUMAN    351    599             
DBREF  5YDR D    1    73  UNP    J3QS39   J3QS39_HUMAN     1     73             
SEQADV 5YDR ALA A   -1  UNP  J3QS39              EXPRESSION TAG                 
SEQADV 5YDR HIS A    0  UNP  J3QS39              EXPRESSION TAG                 
SEQADV 5YDR MET B  350  UNP  P26358              EXPRESSION TAG                 
SEQADV 5YDR ALA D   -1  UNP  J3QS39              EXPRESSION TAG                 
SEQADV 5YDR HIS D    0  UNP  J3QS39              EXPRESSION TAG                 
SEQRES   1 A   75  ALA HIS MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS          
SEQRES   2 A   75  THR ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU          
SEQRES   3 A   75  ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO          
SEQRES   4 A   75  PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU          
SEQRES   5 A   75  GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS          
SEQRES   6 A   75  GLU SER THR LEU HIS LEU VAL LEU ARG LEU                      
SEQRES   1 B  250  MET PRO LYS CYS ILE GLN CYS GLY GLN TYR LEU ASP ASP          
SEQRES   2 B  250  PRO ASP LEU LYS TYR GLY GLN HIS PRO PRO ASP ALA VAL          
SEQRES   3 B  250  ASP GLU PRO GLN MET LEU THR ASN GLU LYS LEU SER ILE          
SEQRES   4 B  250  PHE ASP ALA ASN GLU SER GLY PHE GLU SER TYR GLU ALA          
SEQRES   5 B  250  LEU PRO GLN HIS LYS LEU THR CYS PHE SER VAL TYR CYS          
SEQRES   6 B  250  LYS HIS GLY HIS LEU CYS PRO ILE ASP THR GLY LEU ILE          
SEQRES   7 B  250  GLU LYS ASN ILE GLU LEU PHE PHE SER GLY SER ALA LYS          
SEQRES   8 B  250  PRO ILE TYR ASP ASP ASP PRO SER LEU GLU GLY GLY VAL          
SEQRES   9 B  250  ASN GLY LYS ASN LEU GLY PRO ILE ASN GLU TRP TRP ILE          
SEQRES  10 B  250  THR GLY PHE ASP GLY GLY GLU LYS ALA LEU ILE GLY PHE          
SEQRES  11 B  250  SER THR SER PHE ALA GLU TYR ILE LEU MET ASP PRO SER          
SEQRES  12 B  250  PRO GLU TYR ALA PRO ILE PHE GLY LEU MET GLN GLU LYS          
SEQRES  13 B  250  ILE TYR ILE SER LYS ILE VAL VAL GLU PHE LEU GLN SER          
SEQRES  14 B  250  ASN SER ASP SER THR TYR GLU ASP LEU ILE ASN LYS ILE          
SEQRES  15 B  250  GLU THR THR VAL PRO PRO SER GLY LEU ASN LEU ASN ARG          
SEQRES  16 B  250  PHE THR GLU ASP SER LEU LEU ARG HIS ALA GLN PHE VAL          
SEQRES  17 B  250  VAL GLU GLN VAL GLU SER TYR ASP GLU ALA GLY ASP SER          
SEQRES  18 B  250  ASP GLU GLN PRO ILE PHE LEU THR PRO CYS MET ARG ASP          
SEQRES  19 B  250  LEU ILE LYS LEU ALA GLY VAL THR LEU GLY GLN ARG ARG          
SEQRES  20 B  250  ALA GLN ALA                                                  
SEQRES   1 D   75  ALA HIS MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS          
SEQRES   2 D   75  THR ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU          
SEQRES   3 D   75  ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO          
SEQRES   4 D   75  PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU          
SEQRES   5 D   75  GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS          
SEQRES   6 D   75  GLU SER THR LEU HIS LEU VAL LEU ARG LEU                      
HET    PO4  A 101       5                                                       
HET     ZN  B 601       1                                                       
HET    PO4  B 602       5                                                       
HETNAM     PO4 PHOSPHATE ION                                                    
HETNAM      ZN ZINC ION                                                         
FORMUL   4  PO4    2(O4 P 3-)                                                   
FORMUL   5   ZN    ZN 2+                                                        
FORMUL   7  HOH   *235(H2 O)                                                    
HELIX    1 AA1 THR A   22  GLY A   35  1                                  14    
HELIX    2 AA2 PRO A   37  ASP A   39  5                                   3    
HELIX    3 AA3 ASP B  362  LYS B  366  5                                   5    
HELIX    4 AA4 ASP B  376  THR B  382  1                                   7    
HELIX    5 AA5 ASN B  383  SER B  387  5                                   5    
HELIX    6 AA6 TYR B  495  MET B  502  1                                   8    
HELIX    7 AA7 MET B  502  ASN B  519  1                                  18    
HELIX    8 AA8 THR B  523  THR B  534  1                                  12    
HELIX    9 AA9 THR B  546  HIS B  553  1                                   8    
HELIX   10 AB1 HIS B  553  GLY B  568  1                                  16    
HELIX   11 AB2 THR B  578  GLY B  589  1                                  12    
HELIX   12 AB3 THR B  591  GLN B  598  1                                   8    
HELIX   13 AB4 THR D   22  GLY D   35  1                                  14    
HELIX   14 AB5 PRO D   37  ASP D   39  5                                   3    
HELIX   15 AB6 THR D   55  ASN D   60  5                                   6    
SHEET    1 AA1 5 THR A  12  VAL A  17  0                                        
SHEET    2 AA1 5 MET A   1  LYS A   6 -1  N  MET A   1   O  VAL A  17           
SHEET    3 AA1 5 THR A  66  LEU A  71  1  O  LEU A  67   N  PHE A   4           
SHEET    4 AA1 5 GLN A  41  PHE A  45 -1  N  ARG A  42   O  VAL A  70           
SHEET    5 AA1 5 LYS A  48  GLN A  49 -1  O  LYS A  48   N  PHE A  45           
SHEET    1 AA2 6 VAL B 453  LEU B 458  0                                        
SHEET    2 AA2 6 LEU B 433  LYS B 440 -1  N  PHE B 435   O  LEU B 458           
SHEET    3 AA2 6 GLN B 404  CYS B 414 -1  N  TYR B 413   O  PHE B 434           
SHEET    4 AA2 6 GLU B 485  LEU B 488  1  O  ILE B 487   N  HIS B 405           
SHEET    5 AA2 6 LEU B 476  SER B 480 -1  N  PHE B 479   O  TYR B 486           
SHEET    6 AA2 6 GLU B 463  THR B 467 -1  N  THR B 467   O  LEU B 476           
SHEET    1 AA3 5 THR D  12  VAL D  17  0                                        
SHEET    2 AA3 5 MET D   1  THR D   7 -1  N  MET D   1   O  VAL D  17           
SHEET    3 AA3 5 THR D  66  LEU D  71  1  O  LEU D  67   N  PHE D   4           
SHEET    4 AA3 5 GLN D  41  PHE D  45 -1  N  ARG D  42   O  VAL D  70           
SHEET    5 AA3 5 LYS D  48  GLN D  49 -1  O  LYS D  48   N  PHE D  45           
LINK         SG  CYS B 353                ZN    ZN B 601     1555   1555  2.39  
LINK         SG  CYS B 356                ZN    ZN B 601     1555   1555  2.26  
LINK         SG  CYS B 414                ZN    ZN B 601     1555   1555  2.30  
LINK         ND1 HIS B 418                ZN    ZN B 601     1555   1555  2.13  
CISPEP   1 GLY B  459    PRO B  460          0         5.90                     
SITE     1 AC1  3 ALA A  -1  HIS A   0  LYS B 415                               
SITE     1 AC2  4 CYS B 353  CYS B 356  CYS B 414  HIS B 418                    
SITE     1 AC3  2 HIS B 370  ASN B 457                                          
CRYST1  131.760  131.760   61.025  90.00  90.00 120.00 P 65         12          
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      0.007590  0.004382  0.000000        0.00000                         
SCALE2      0.000000  0.008764  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.016387        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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