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Database: PDB
Entry: 2VQW
LinkDB: 2VQW
Original site: 2VQW 
HEADER    HYDROLASE                               19-MAR-08   2VQW              
TITLE     STRUCTURE OF INHIBITOR-FREE HDAC4 CATALYTIC DOMAIN (WITH              
TITLE    2 GAIN-OF-FUNCTION MUTATION HIS332TYR)                                 
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: HISTONE DEACETYLASE 4;                                     
COMPND   3 CHAIN: G;                                                            
COMPND   4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 648-1057;                       
COMPND   5 SYNONYM: HD4;                                                        
COMPND   6 EC: 3.5.1.98;                                                        
COMPND   7 ENGINEERED: YES;                                                     
COMPND   8 MUTATION: YES                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);                                 
SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PETM-11 (OBTAINED FROM EMBL-              
SOURCE   9  HEIDELBERG)                                                         
KEYWDS    INHIBITOR, REPRESSOR, CHROMATIN, COILED COIL, HISTONE                 
KEYWDS   2 DEACETYLASE, TRANSCRIPTION REGULATION, UBL CONJUGATION,              
KEYWDS   3 CHROMATIN REGULATOR, POLYMORPHISM, TRANSCRIPTION,                    
KEYWDS   4 PHOSPHOPROTEIN, HDAC, ZINC, HDACI, NUCLEUS, HYDROLASE,               
KEYWDS   5 CYTOPLASM                                                            
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    M.J.BOTTOMLEY,P.LO SURDO,P.DI GIOVINE,A.CIRILLO,R.SCARPELLI,          
AUTHOR   2 F.FERRIGNO,P.JONES,P.NEDDERMANN,R.DE FRANCESCO,                      
AUTHOR   3 C.STEINKUHLER,P.GALLINARI,A.CARFI                                    
REVDAT   3   24-FEB-09 2VQW    1       VERSN                                    
REVDAT   2   30-SEP-08 2VQW    1       JRNL                                     
REVDAT   1   05-AUG-08 2VQW    0                                                
JRNL        AUTH   M.J.BOTTOMLEY,P.LO SURDO,P.DI GIOVINE,A.CIRILLO,             
JRNL        AUTH 2 R.SCARPELLI,F.FERRIGNO,P.JONES,P.NEDDERMANN,                 
JRNL        AUTH 3 R.DE FRANCESCO,C.STEINKUHLER,P.GALLINARI,A.CARFI             
JRNL        TITL   STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE HUMAN              
JRNL        TITL 2 HDAC4 CATALYTIC DOMAIN REVEALS A REGULATORY                  
JRNL        TITL 3 STRUCTURAL ZINC-BINDING DOMAIN.                              
JRNL        REF    J.BIOL.CHEM.                  V. 283 26694 2008              
JRNL        REFN                   ISSN 0021-9258                               
JRNL        PMID   18614528                                                     
JRNL        DOI    10.1074/JBC.M803514200                                       
REMARK   2                                                                      
REMARK   2 RESOLUTION.    3.0  ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : REFMAC 5.2.0019                                      
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON                               
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL                           
REMARK   3   COMPLETENESS FOR RANGE        (%) : 100.0                          
REMARK   3   NUMBER OF REFLECTIONS             : 14460                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.234                           
REMARK   3   R VALUE            (WORKING SET) : 0.233                           
REMARK   3   FREE R VALUE                     : 0.261                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.000                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 756                             
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 20                           
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 3.00                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 3.08                         
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 1035                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 100.00                       
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3340                       
REMARK   3   BIN FREE R VALUE SET COUNT          : 56                           
REMARK   3   BIN FREE R VALUE                    : 0.3630                       
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 2868                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 4                                       
REMARK   3   SOLVENT ATOMS            : 0                                       
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 83.60                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : 4.51000                                              
REMARK   3    B22 (A**2) : 4.51000                                              
REMARK   3    B33 (A**2) : -6.76000                                             
REMARK   3    B12 (A**2) : 2.25000                                              
REMARK   3    B13 (A**2) : 0.00000                                              
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.                                 
REMARK   3   ESU BASED ON R VALUE                            (A): 0.702         
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.356         
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.314         
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.230        
REMARK   3                                                                      
REMARK   3 CORRELATION COEFFICIENTS.                                            
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.933                         
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.923                         
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT      
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  2936 ; 0.006 ; 0.021       
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  3991 ; 1.033 ; 1.953       
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL       
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   380 ; 5.326 ; 5.000       
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   124 ;36.936 ;23.790       
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   449 ;17.237 ;15.000       
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    17 ;11.797 ;15.000       
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   450 ; 0.070 ; 0.200       
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2248 ; 0.002 ; 0.020       
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1432 ; 0.203 ; 0.200       
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  1999 ; 0.297 ; 0.200       
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):    74 ; 0.140 ; 0.200       
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL       
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):     6 ; 0.098 ; 0.200       
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):    24 ; 0.136 ; 0.200       
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):     2 ; 0.195 ; 0.200       
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT      
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  1892 ; 0.298 ; 1.500       
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  3024 ; 0.552 ; 2.000       
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1055 ; 0.486 ; 3.000       
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):   967 ; 0.823 ; 4.500       
REMARK   3                                                                      
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT       
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS STATISTICS                                           
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL                              
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED : MASK                                                 
REMARK   3   PARAMETERS FOR MASK CALCULATION                                    
REMARK   3   VDW PROBE RADIUS   : 1.20                                          
REMARK   3   ION PROBE RADIUS   : 0.80                                          
REMARK   3   SHRINKAGE RADIUS   : 0.80                                          
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE          
REMARK   3  RIDING POSITIONS                                                    
REMARK   4                                                                      
REMARK   4 2VQW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAR-08.                  
REMARK 100 THE PDBE ID CODE IS EBI-35736.                                       
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 10-JUL-06                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : ESRF                               
REMARK 200  BEAMLINE                       : ID29                               
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.07                               
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ADSC                               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM                             
REMARK 200  DATA SCALING SOFTWARE          : SCALA                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 15460                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 3.00                               
REMARK 200  RESOLUTION RANGE LOW       (A) : 60.00                              
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NONE                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 100.0                              
REMARK 200  DATA REDUNDANCY                : 7.1                                
REMARK 200  R MERGE                    (I) : 0.15                               
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 14.30                              
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 3.48                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0                              
REMARK 200  DATA REDUNDANCY IN SHELL       : 7.2                                
REMARK 200  R MERGE FOR SHELL          (I) : 0.84                               
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 2.20                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER                                                
REMARK 200 STARTING MODEL: PDB ENTRY 2VQJ                                       
REMARK 200                                                                      
REMARK 200 REMARK: NONE                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 71                                        
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.9                      
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 18% PEG 10000,        
REMARK 280  1MM DTT                                                             
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       46.34600            
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       23.17300            
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       34.75950            
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       11.58650            
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       57.93250            
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 GENERATING THE BIOMOLECULE                                           
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: MONOMERIC                         
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PQS                                                   
REMARK 350 APPLY THE FOLLOWING TO CHAINS: G                                     
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 400                                                                      
REMARK 400 COMPOUND                                                             
REMARK 400 ENGINEERED RESIDUE IN CHAIN G, HIS 976 TO TYR                        
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     GLY G     1                                                      
REMARK 465     ALA G     2                                                      
REMARK 465     MET G     3                                                      
REMARK 465     THR G     4                                                      
REMARK 465     LYS G     5                                                      
REMARK 465     PRO G     6                                                      
REMARK 465     GLY G    26                                                      
REMARK 465     SER G    27                                                      
REMARK 465     SER G    28                                                      
REMARK 465     ASN G    85                                                      
REMARK 465     ARG G    86                                                      
REMARK 465     GLN G    87                                                      
REMARK 465     LYS G    88                                                      
REMARK 465     LEU G    89                                                      
REMARK 465     ASP G    90                                                      
REMARK 465     SER G    91                                                      
REMARK 465     LYS G    92                                                      
REMARK 465     LYS G    93                                                      
REMARK 465     LEU G    94                                                      
REMARK 465     LEU G    95                                                      
REMARK 465     GLY G    96                                                      
REMARK 465     SER G    97                                                      
REMARK 465     LEU G    98                                                      
REMARK 465     ALA G    99                                                      
REMARK 465     GLU G   407                                                      
REMARK 465     GLU G   408                                                      
REMARK 465     ALA G   409                                                      
REMARK 465     GLU G   410                                                      
REMARK 465     THR G   411                                                      
REMARK 465     VAL G   412                                                      
REMARK 465     THR G   413                                                      
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 G  20    CG   CD   CE   NZ                                   
REMARK 470     ARG G  51    CG   CD   NE   CZ   NH1  NH2                        
REMARK 470     LYS G  53    CG   CD   CE   NZ                                   
REMARK 470     GLU G 120    CG   CD   OE1  OE2                                  
REMARK 470     ARG G 389    CG   CD   NE   CZ   NH1  NH2                        
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 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    HIS G  21       87.91    -66.87                                   
REMARK 500    PRO G  83     -149.62    -87.89                                   
REMARK 500    ARG G 184      -81.52    -84.47                                   
REMARK 500    TYR G 208       -6.26    -57.17                                   
REMARK 500    VAL G 271      -71.85    -61.85                                   
REMARK 500    ALA G 279       79.08     43.29                                   
REMARK 500    PHE G 289       44.75   -104.76                                   
REMARK 500    PRO G 357      137.80    -37.82                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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                               K G1407   K                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 ASP G 194   O                                                      
REMARK 620 2 ASP G 194   OD1  66.0                                              
REMARK 620 3 ASP G 196   O   103.0  95.7                                        
REMARK 620 4 HIS G 198   O   162.9  97.8  72.2                                  
REMARK 620 5 LEU G 218   O    76.7 132.3  64.1 113.9                            
REMARK 620 6 SER G 217   OG   81.2 107.8 155.5 110.1  94.2                      
REMARK 620 N                    1     2     3     4     5                       
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                               K G1408   K                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 PHE G 207   O                                                      
REMARK 620 2 ASP G 210   O    78.7                                              
REMARK 620 3 VAL G 213   O   114.6  61.0                                        
REMARK 620 4 PHE G 244   O   169.9 111.4  72.5                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN G1409  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 ASP G 290   OD2                                                    
REMARK 620 2 HIS G 198   ND1  97.1                                              
REMARK 620 3 ASP G 196   OD2 106.9  98.9                                        
REMARK 620 N                    1     2                                         
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN G1410  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS G  25   SG                                                     
REMARK 620 2 CYS G  23   SG   96.0                                              
REMARK 620 3 HIS G  31   NE2 131.4 113.1                                        
REMARK 620 4 CYS G 107   SG  103.1 111.0 101.4                                  
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   K G1407                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE   K G1408                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  ZN G1409                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC4                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  ZN G1410                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 2VQQ   RELATED DB: PDB                                   
REMARK 900  STRUCTURE OF HDAC4 CATALYTIC DOMAIN (A                              
REMARK 900  DOUBLE CYSTEINE-TO-ALANINE MUTANT) BOUND TO                         
REMARK 900   A TRIFLUOROMETHYLKETONE INHBITOR                                   
REMARK 900 RELATED ID: 2VQO   RELATED DB: PDB                                   
REMARK 900  STRUCTURE OF HDAC4 CATALYTIC DOMAIN WITH A                          
REMARK 900  GAIN-OF-FUNCTION MUATION BOUND TO A                                 
REMARK 900  TRIFLUOROMETHYLKETONE INHBITOR                                      
REMARK 900 RELATED ID: 2VQV   RELATED DB: PDB                                   
REMARK 900  STRUCTURE OF HDAC4 CATALYTIC DOMAIN WITH A                          
REMARK 900  GAIN-OF-FUNCTION MUATION BOUND TO A                                 
REMARK 900  HYDROXAMIC ACID INHIBITOR                                           
REMARK 900 RELATED ID: 2VQM   RELATED DB: PDB                                   
REMARK 900  STRUCTURE OF HDAC4 CATALYTIC DOMAIN BOUND TO                        
REMARK 900   A HYDROXAMIC ACID INHBITOR                                         
REMARK 900 RELATED ID: 2VQJ   RELATED DB: PDB                                   
REMARK 900  STRUCTURE OF HDAC4 CATALYTIC DOMAIN BOUND TO                        
REMARK 900   A TRIFLUOROMETHYLKETONE INHBITOR                                   
DBREF  2VQW G    1     3  PDB    2VQW     2VQW             1      3             
DBREF  2VQW G    4   413  UNP    P56524   HDAC4_HUMAN    648   1057             
SEQADV 2VQW TYR G  332  UNP  P56524    HIS   976 ENGINEERED MUTATION            
SEQRES   1 G  413  GLY ALA MET THR LYS PRO ARG PHE THR THR GLY LEU VAL          
SEQRES   2 G  413  TYR ASP THR LEU MET LEU LYS HIS GLN CYS THR CYS GLY          
SEQRES   3 G  413  SER SER SER SER HIS PRO GLU HIS ALA GLY ARG ILE GLN          
SEQRES   4 G  413  SER ILE TRP SER ARG LEU GLN GLU THR GLY LEU ARG GLY          
SEQRES   5 G  413  LYS CYS GLU CYS ILE ARG GLY ARG LYS ALA THR LEU GLU          
SEQRES   6 G  413  GLU LEU GLN THR VAL HIS SER GLU ALA HIS THR LEU LEU          
SEQRES   7 G  413  TYR GLY THR ASN PRO LEU ASN ARG GLN LYS LEU ASP SER          
SEQRES   8 G  413  LYS LYS LEU LEU GLY SER LEU ALA SER VAL PHE VAL ARG          
SEQRES   9 G  413  LEU PRO CYS GLY GLY VAL GLY VAL ASP SER ASP THR ILE          
SEQRES  10 G  413  TRP ASN GLU VAL HIS SER ALA GLY ALA ALA ARG LEU ALA          
SEQRES  11 G  413  VAL GLY CYS VAL VAL GLU LEU VAL PHE LYS VAL ALA THR          
SEQRES  12 G  413  GLY GLU LEU LYS ASN GLY PHE ALA VAL VAL ARG PRO PRO          
SEQRES  13 G  413  GLY HIS HIS ALA GLU GLU SER THR PRO MET GLY PHE CYS          
SEQRES  14 G  413  TYR PHE ASN SER VAL ALA VAL ALA ALA LYS LEU LEU GLN          
SEQRES  15 G  413  GLN ARG LEU SER VAL SER LYS ILE LEU ILE VAL ASP TRP          
SEQRES  16 G  413  ASP VAL HIS HIS GLY ASN GLY THR GLN GLN ALA PHE TYR          
SEQRES  17 G  413  SER ASP PRO SER VAL LEU TYR MET SER LEU HIS ARG TYR          
SEQRES  18 G  413  ASP ASP GLY ASN PHE PHE PRO GLY SER GLY ALA PRO ASP          
SEQRES  19 G  413  GLU VAL GLY THR GLY PRO GLY VAL GLY PHE ASN VAL ASN          
SEQRES  20 G  413  MET ALA PHE THR GLY GLY LEU ASP PRO PRO MET GLY ASP          
SEQRES  21 G  413  ALA GLU TYR LEU ALA ALA PHE ARG THR VAL VAL MET PRO          
SEQRES  22 G  413  ILE ALA SER GLU PHE ALA PRO ASP VAL VAL LEU VAL SER          
SEQRES  23 G  413  SER GLY PHE ASP ALA VAL GLU GLY HIS PRO THR PRO LEU          
SEQRES  24 G  413  GLY GLY TYR ASN LEU SER ALA ARG CYS PHE GLY TYR LEU          
SEQRES  25 G  413  THR LYS GLN LEU MET GLY LEU ALA GLY GLY ARG ILE VAL          
SEQRES  26 G  413  LEU ALA LEU GLU GLY GLY TYR ASP LEU THR ALA ILE CYS          
SEQRES  27 G  413  ASP ALA SER GLU ALA CYS VAL SER ALA LEU LEU GLY ASN          
SEQRES  28 G  413  GLU LEU ASP PRO LEU PRO GLU LYS VAL LEU GLN GLN ARG          
SEQRES  29 G  413  PRO ASN ALA ASN ALA VAL ARG SER MET GLU LYS VAL MET          
SEQRES  30 G  413  GLU ILE HIS SER LYS TYR TRP ARG CYS LEU GLN ARG THR          
SEQRES  31 G  413  THR SER THR ALA GLY ARG SER LEU ILE GLU ALA GLN THR          
SEQRES  32 G  413  CYS GLU ASN GLU GLU ALA GLU THR VAL THR                      
HET      K  G1407       1                                                       
HET      K  G1408       1                                                       
HET     ZN  G1409       1                                                       
HET     ZN  G1410       1                                                       
HETNAM       K POTASSIUM ION                                                    
HETNAM      ZN ZINC ION                                                         
FORMUL   2    K    2(K 1+)                                                      
FORMUL   3   ZN    2(ZN 2+)                                                     
HELIX    1   1 ASP G   15  HIS G   21  5                                   7    
HELIX    2   2 ALA G   35  THR G   48  1                                  14    
HELIX    3   3 THR G   63  GLN G   68  1                                   6    
HELIX    4   4 SER G   72  THR G   81  1                                  10    
HELIX    5   5 HIS G  122  THR G  143  1                                  22    
HELIX    6   6 ASN G  172  ARG G  184  1                                  13    
HELIX    7   7 GLY G  200  TYR G  208  1                                   9    
HELIX    8   8 ASP G  222  ASN G  225  5                                   4    
HELIX    9   9 THR G  238  VAL G  242  5                                   5    
HELIX   10  10 GLY G  259  VAL G  270  1                                  12    
HELIX   11  11 VAL G  270  ALA G  279  1                                  10    
HELIX   12  12 SER G  305  GLY G  318  1                                  14    
HELIX   13  13 ASP G  333  GLY G  350  1                                  18    
HELIX   14  14 PRO G  357  GLN G  363  1                                   7    
HELIX   15  15 ASN G  366  SER G  381  1                                  16    
HELIX   16  16 SER G  397  ASN G  406  1                                  10    
SHEET    1  GA 8 GLU G  55  ILE G  57  0                                        
SHEET    2  GA 8 THR G  10  VAL G  13  1  O  THR G  10   N  GLU G  55           
SHEET    3  GA 8 ASN G 148  ALA G 151  1  O  ASN G 148   N  GLY G  11           
SHEET    4  GA 8 ILE G 324  LEU G 328  1  O  ILE G 324   N  GLY G 149           
SHEET    5  GA 8 VAL G 282  SER G 287  1  O  VAL G 283   N  VAL G 325           
SHEET    6  GA 8 ILE G 190  ASP G 194  1  O  LEU G 191   N  LEU G 284           
SHEET    7  GA 8 VAL G 213  ARG G 220  1  O  LEU G 214   N  ILE G 192           
SHEET    8  GA 8 ASN G 245  PHE G 250  1  O  VAL G 246   N  SER G 217           
SHEET    1  GB 2 VAL G 103  ARG G 104  0                                        
SHEET    2  GB 2 VAL G 110  GLY G 111 -1  O  GLY G 111   N  VAL G 103           
LINK         K     K G1407                 O   ASP G 194     1555   1555  3.16  
LINK         K     K G1407                 OD1 ASP G 194     1555   1555  2.94  
LINK         K     K G1407                 O   ASP G 196     1555   1555  2.64  
LINK         K     K G1407                 O   HIS G 198     1555   1555  2.64  
LINK         K     K G1407                 O   LEU G 218     1555   1555  3.26  
LINK         K     K G1407                 OG  SER G 217     1555   1555  2.87  
LINK         K     K G1408                 O   PHE G 207     1555   1555  2.75  
LINK         K     K G1408                 O   ASP G 210     1555   1555  2.97  
LINK         K     K G1408                 O   VAL G 213     1555   1555  3.12  
LINK         K     K G1408                 O   PHE G 244     1555   1555  3.36  
LINK        ZN    ZN G1409                 ND1 HIS G 198     1555   1555  2.00  
LINK        ZN    ZN G1409                 OD2 ASP G 196     1555   1555  1.95  
LINK        ZN    ZN G1409                 OD2 ASP G 290     1555   1555  1.96  
LINK        ZN    ZN G1410                 SG  CYS G  23     1555   1555  2.35  
LINK        ZN    ZN G1410                 NE2 HIS G  31     1555   1555  2.11  
LINK        ZN    ZN G1410                 SG  CYS G 107     1555   1555  2.34  
LINK        ZN    ZN G1410                 SG  CYS G  25     1555   1555  2.49  
CISPEP   1 ARG G  154    PRO G  155          0         1.75                     
CISPEP   2 PHE G  227    PRO G  228          0        -1.57                     
CISPEP   3 ASP G  255    PRO G  256          0        -8.94                     
SITE     1 AC1  5 ASP G 194  ASP G 196  HIS G 198  SER G 217                    
SITE     2 AC1  5 LEU G 218                                                     
SITE     1 AC2  4 PHE G 207  ASP G 210  VAL G 213  PHE G 244                    
SITE     1 AC3  3 ASP G 196  HIS G 198  ASP G 290                               
SITE     1 AC4  4 CYS G  23  CYS G  25  HIS G  31  CYS G 107                    
CRYST1  137.911  137.911   69.519  90.00  90.00 120.00 P 65          6          
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      0.007251  0.004186  0.000000        0.00000                         
SCALE2      0.000000  0.008373  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.014385        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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