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Database: PDB
Entry: 5B8D
LinkDB: 5B8D
Original site: 5B8D 
HEADER    HYDROLASE                               14-JUN-16   5B8D              
TITLE     CRYSTAL STRUCTURE OF A LOW OCCUPANCY FRAGMENT CANDIDATE (N-(4-METHYL- 
TITLE    2 1,3-THIAZOL-2-YL)PROPANAMIDE) BOUND ADJACENT TO THE UBIQUITIN BINDING
TITLE    3 POCKET OF THE HDAC6 ZINC-FINGER DOMAIN                               
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: HISTONE DEACETYLASE 6;                                     
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: HD6;                                                        
COMPND   5 EC: 3.5.1.98;                                                        
COMPND   6 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: HDAC6, KIAA0901, JM21;                                         
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON PLUS;                     
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PET28-LIC                                 
KEYWDS    HISTONE DEACETYLASE, HDAC, HDAC6, FRAGMENT SCREENING, STRUCTURAL      
KEYWDS   2 GENOMICS CONSORTIUM, SGC, DIAMOND I04-1 XCHEM, PANDDA, HYDROLASE     
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    R.J.HARDING,W.TEMPEL,P.COLLINS,N.PEARCE,J.BRANDAO-NETO,A.DOUANGAMATH, 
AUTHOR   2 M.RAVICHANDRAN,M.SCHAPIRA,C.BOUNTRA,A.M.EDWARDS,F.VON DELFT,         
AUTHOR   3 V.SANTHAKUMAR,C.M.ARROWSMITH,STRUCTURAL GENOMICS CONSORTIUM (SGC)    
REVDAT   3   27-FEB-19 5B8D    1       JRNL                                     
REVDAT   2   21-MAR-18 5B8D    1       JRNL   REMARK                            
REVDAT   1   27-JUL-16 5B8D    0                                                
JRNL        AUTH   R.J.HARDING,R.FERREIRA DE FREITAS,P.COLLINS,I.FRANZONI,      
JRNL        AUTH 2 M.RAVICHANDRAN,H.OUYANG,K.A.JUAREZ-ORNELAS,M.LAUTENS,        
JRNL        AUTH 3 M.SCHAPIRA,F.VON DELFT,V.SANTHAKUMAR,C.H.ARROWSMITH          
JRNL        TITL   SMALL MOLECULE ANTAGONISTS OF THE INTERACTION BETWEEN THE    
JRNL        TITL 2 HISTONE DEACETYLASE 6 ZINC-FINGER DOMAIN AND UBIQUITIN.      
JRNL        REF    J. MED. CHEM.                 V.  60  9090 2017              
JRNL        REFN                   ISSN 1520-4804                               
JRNL        PMID   29019676                                                     
JRNL        DOI    10.1021/ACS.JMEDCHEM.7B00933                                 
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.05 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : REFMAC 5.8.0151                                      
REMARK   3   AUTHORS     : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,              
REMARK   3               : NICHOLLS,WINN,LONG,VAGIN                             
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.05                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 34.80                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.2                           
REMARK   3   NUMBER OF REFLECTIONS             : 45286                          
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) : 0.129                           
REMARK   3   R VALUE            (WORKING SET) : 0.128                           
REMARK   3   FREE R VALUE                     : 0.146                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.600                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 2178                            
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) : 1.05                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.08                         
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 2787                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 82.35                        
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2950                       
REMARK   3   BIN FREE R VALUE SET COUNT          : 152                          
REMARK   3   BIN FREE R VALUE                    : 0.3050                       
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 779                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 56                                      
REMARK   3   SOLVENT ATOMS            : 79                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 13.19                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -0.21000                                             
REMARK   3    B22 (A**2) : 0.67000                                              
REMARK   3    B33 (A**2) : -0.46000                                             
REMARK   3    B12 (A**2) : 0.00000                                              
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): 0.023         
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.023         
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.016         
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.733         
REMARK   3                                                                      
REMARK   3 CORRELATION COEFFICIENTS.                                            
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.980                         
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.977                         
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT      
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):   918 ; 0.016 ; 0.019       
REMARK   3   BOND LENGTHS OTHERS               (A):   822 ; 0.003 ; 0.020       
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  1270 ; 1.504 ; 1.901       
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  1897 ; 1.098 ; 3.000       
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   119 ; 6.624 ; 5.000       
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):    44 ;34.210 ;25.000       
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   131 ;11.047 ;15.000       
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):     1 ; 6.140 ;15.000       
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   135 ; 0.110 ; 0.200       
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  1124 ; 0.010 ; 0.021       
REMARK   3   GENERAL PLANES OTHERS             (A):   235 ; 0.002 ; 0.020       
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):  NULL ;  NULL ;  NULL       
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL       
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL       
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):  NULL ;  NULL ;  NULL       
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):   438 ; 0.862 ; 1.100       
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):   439 ; 0.886 ; 1.099       
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):   555 ; 1.177 ; 1.663       
REMARK   3   MAIN-CHAIN ANGLE OTHER ATOMS   (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN ANGLE OTHER ATOMS   (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   LONG RANGE B REFINED ATOMS     (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   LONG RANGE B OTHER ATOMS       (A**2):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT       
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  1740 ; 1.543 ; 3.000       
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):    29 ;20.677 ; 5.000       
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  1792 ; 5.867 ; 5.000       
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: USERS OF THIS CRYSTAL STRUCTURE: VERIFY   
REMARK   3  OUR INTEPRETION OF THE ELECTRON DENSITY. AMPLITUDES AND UNMERGED    
REMARK   3  INTENSITIES ARE INCLUDED WITH THIS DEPOSITION. DIFFRACTION          
REMARK   3  IMAGES WILL BE DEPOSITED IN A PUBLIC REPOSITORY. GEOMETRY           
REMARK   3  RESTRAINTS FOR THE FRAGMENT CANDIDATE WERE PREPARED WITH GRADE.     
REMARK   3  THE METHYL GROUP OF THE FRAGMENT CANDIDATE WAS NOT RESOLVED BY      
REMARK   3  ELECTRON DENSITY AND WAS OMITTED FROM THE MODEL. AMBIGUOUS          
REMARK   3  DIFFERENCE DENSITY SUGGESTS SOME FORM OF COVALENT MODIFICATION      
REMARK   3  OF CYS1147.                                                         
REMARK   4                                                                      
REMARK   4 5B8D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-16.                  
REMARK 100 THE DEPOSITION ID IS D_1300000718.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 30-SEP-15                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 4.6                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : DIAMOND                            
REMARK 200  BEAMLINE                       : I04-1                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.92819                            
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS 6M-F               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : AIMLESS 0.5.26                     
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 47523                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.050                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 34.800                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 97.4                               
REMARK 200  DATA REDUNDANCY                : 5.400                              
REMARK 200  R MERGE                    (I) : 0.05800                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 14.6000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.07                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 79.1                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.40                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.89300                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 1.000                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL                         
REMARK 200 SOFTWARE USED: NULL                                                  
REMARK 200 STARTING MODEL: PDBID 3C5K                                           
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 43.26                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 2M NA-FORMATE, 0.2M NA-ACETATE PH4.6,    
REMARK 280  5% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE      
REMARK 280  291K                                                                
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
REMARK 290       4555   X+1/2,-Y+1/2,-Z                                         
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       20.71700            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       28.27450            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       22.07850            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       28.27450            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       20.71700            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       22.07850            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
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: MONOMERIC                         
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 520 ANGSTROM**2                           
REMARK 350 SURFACE AREA OF THE COMPLEX: 5900 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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     GLY A  1107                                                      
REMARK 465     SER A  1108                                                      
REMARK 465     GLU A  1209                                                      
REMARK 465     ASP A  1210                                                      
REMARK 465     MET A  1211                                                      
REMARK 465     PRO A  1212                                                      
REMARK 465     HIS A  1213                                                      
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     GLY A1208    CA   C    O                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   SG   CYS A  1148     UNK  UNX A  1313              1.51            
REMARK 500   O    GLN A  1140     UNK  UNX A  1325              1.55            
REMARK 500   SG   CYS A  1148     UNK  UNX A  1314              1.56            
REMARK 500   UNK  UNX A  1309     UNK  UNX A  1326              1.70            
REMARK 500   OD1  ASN A  1205     O    HOH A  1401              1.76            
REMARK 500   UNK  UNX A  1326     UNK  UNX A  1341              1.84            
REMARK 500   OD1  ASN A  1205     O    HOH A  1402              2.13            
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    ASP A1135      -62.34    -95.94                                   
REMARK 500    ILE A1157     -104.29    -94.08                                   
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                              ZN A1303  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A1113   SG                                                     
REMARK 620 2 HIS A1115   ND1 109.5                                              
REMARK 620 3 CYS A1183   SG  116.5  99.6                                        
REMARK 620 4 CYS A1186   SG  111.7 105.8 112.6                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN A1302  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A1133   SG                                                     
REMARK 620 2 CYS A1136   SG  109.3                                              
REMARK 620 3 CYS A1153   SG  113.4 114.6                                        
REMARK 620 4 HIS A1160   ND1 106.8 111.2 101.1                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN A1301  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A1145   SG                                                     
REMARK 620 2 HIS A1164   NE2 116.2                                              
REMARK 620 3 HIS A1170   ND1 110.0 112.0                                        
REMARK 620 N                    1     2                                         
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              NA A1343  NA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 TYR A1156   O                                                      
REMARK 620 2 ILE A1157   O    85.3                                              
REMARK 620 3 HOH A1449   O    88.9  91.6                                        
REMARK 620 4 HOH A1469   O   176.6  92.6  88.5                                  
REMARK 620 5 HOH A1470   O    84.0 169.2  86.5  98.0                            
REMARK 620 N                    1     2     3     4                             
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 1301                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1302                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1303                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC4                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 1304                
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC5                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 1305                
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC6                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue 6T4 A 1306                
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC7                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 1343                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 5KH3   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5KH7   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5KH9   RELATED DB: PDB                                   
DBREF  5B8D A 1109  1213  UNP    Q9UBN7   HDAC6_HUMAN   1109   1213             
SEQADV 5B8D GLY A 1107  UNP  Q9UBN7              EXPRESSION TAG                 
SEQADV 5B8D SER A 1108  UNP  Q9UBN7              EXPRESSION TAG                 
SEQRES   1 A  107  GLY SER PRO LEU PRO TRP CYS PRO HIS LEU VAL ALA VAL          
SEQRES   2 A  107  CYS PRO ILE PRO ALA ALA GLY LEU ASP VAL THR GLN PRO          
SEQRES   3 A  107  CYS GLY ASP CYS GLY THR ILE GLN GLU ASN TRP VAL CYS          
SEQRES   4 A  107  LEU SER CYS TYR GLN VAL TYR CYS GLY ARG TYR ILE ASN          
SEQRES   5 A  107  GLY HIS MET LEU GLN HIS HIS GLY ASN SER GLY HIS PRO          
SEQRES   6 A  107  LEU VAL LEU SER TYR ILE ASP LEU SER ALA TRP CYS TYR          
SEQRES   7 A  107  TYR CYS GLN ALA TYR VAL HIS HIS GLN ALA LEU LEU ASP          
SEQRES   8 A  107  VAL LYS ASN ILE ALA HIS GLN ASN LYS PHE GLY GLU ASP          
SEQRES   9 A  107  MET PRO HIS                                                  
HET     ZN  A1301       1                                                       
HET     ZN  A1302       1                                                       
HET     ZN  A1303       1                                                       
HET    FMT  A1304       3                                                       
HET    FMT  A1305       3                                                       
HET    6T4  A1306      10                                                       
HET    UNX  A1307       1                                                       
HET    UNX  A1308       1                                                       
HET    UNX  A1309       1                                                       
HET    UNX  A1310       1                                                       
HET    UNX  A1311       1                                                       
HET    UNX  A1312       1                                                       
HET    UNX  A1313       1                                                       
HET    UNX  A1314       1                                                       
HET    UNX  A1315       1                                                       
HET    UNX  A1316       1                                                       
HET    UNX  A1317       1                                                       
HET    UNX  A1318       1                                                       
HET    UNX  A1319       1                                                       
HET    UNX  A1320       1                                                       
HET    UNX  A1321       1                                                       
HET    UNX  A1322       1                                                       
HET    UNX  A1323       1                                                       
HET    UNX  A1324       1                                                       
HET    UNX  A1325       1                                                       
HET    UNX  A1326       1                                                       
HET    UNX  A1327       1                                                       
HET    UNX  A1328       1                                                       
HET    UNX  A1329       1                                                       
HET    UNX  A1330       1                                                       
HET    UNX  A1331       1                                                       
HET    UNX  A1332       1                                                       
HET    UNX  A1333       1                                                       
HET    UNX  A1334       1                                                       
HET    UNX  A1335       1                                                       
HET    UNX  A1336       1                                                       
HET    UNX  A1337       1                                                       
HET    UNX  A1338       1                                                       
HET    UNX  A1339       1                                                       
HET    UNX  A1340       1                                                       
HET    UNX  A1341       1                                                       
HET    UNX  A1342       1                                                       
HET     NA  A1343       1                                                       
HETNAM      ZN ZINC ION                                                         
HETNAM     FMT FORMIC ACID                                                      
HETNAM     6T4 ~{N}-(4-METHYL-1,3-THIAZOL-2-YL)ETHANAMIDE                       
HETNAM     UNX UNKNOWN ATOM OR ION                                              
HETNAM      NA SODIUM ION                                                       
FORMUL   2   ZN    3(ZN 2+)                                                     
FORMUL   5  FMT    2(C H2 O2)                                                   
FORMUL   7  6T4    C6 H8 N2 O S                                                 
FORMUL   8  UNX    36(X)                                                        
FORMUL  44   NA    NA 1+                                                        
FORMUL  45  HOH   *79(H2 O)                                                     
HELIX    1 AA1 HIS A 1115  VAL A 1119  5                                   5    
HELIX    2 AA2 GLY A 1159  GLY A 1169  1                                  11    
HELIX    3 AA3 HIS A 1192  ALA A 1194  5                                   3    
HELIX    4 AA4 LEU A 1195  PHE A 1207  1                                  13    
SHEET    1 AA1 5 VAL A1151  CYS A1153  0                                        
SHEET    2 AA1 5 ASN A1142  CYS A1145 -1  N  TRP A1143   O  TYR A1152           
SHEET    3 AA1 5 LEU A1172  SER A1175 -1  O  LEU A1174   N  VAL A1144           
SHEET    4 AA1 5 ALA A1181  CYS A1183 -1  O  TRP A1182   N  VAL A1173           
SHEET    5 AA1 5 ALA A1188  TYR A1189 -1  O  ALA A1188   N  CYS A1183           
LINK         SG  CYS A1113                ZN    ZN A1303     1555   1555  2.36  
LINK         ND1 HIS A1115                ZN    ZN A1303     1555   1555  2.16  
LINK         SG  CYS A1133                ZN    ZN A1302     1555   1555  2.39  
LINK         SG  CYS A1136                ZN    ZN A1302     1555   1555  2.34  
LINK         SG  CYS A1145                ZN    ZN A1301     1555   1555  2.31  
LINK         SG  CYS A1153                ZN    ZN A1302     1555   1555  2.37  
LINK         O   TYR A1156                NA    NA A1343     1555   1555  2.47  
LINK         O   ILE A1157                NA    NA A1343     1555   1555  2.42  
LINK         ND1 HIS A1160                ZN    ZN A1302     1555   1555  2.12  
LINK         NE2 HIS A1164                ZN    ZN A1301     1555   1555  2.09  
LINK         ND1 HIS A1170                ZN    ZN A1301     1555   1555  2.08  
LINK         SG  CYS A1183                ZN    ZN A1303     1555   1555  2.35  
LINK         SG  CYS A1186                ZN    ZN A1303     1555   1555  2.51  
LINK        NA    NA A1343                 O   HOH A1449     1555   1555  2.49  
LINK        NA    NA A1343                 O   HOH A1469     1555   1555  2.45  
LINK        NA    NA A1343                 O   HOH A1470     1555   3555  2.46  
SITE     1 AC1  4 CYS A1145  CYS A1148  HIS A1164  HIS A1170                    
SITE     1 AC2  4 CYS A1133  CYS A1136  CYS A1153  HIS A1160                    
SITE     1 AC3  4 CYS A1113  HIS A1115  CYS A1183  CYS A1186                    
SITE     1 AC4  7 TRP A1143  GLY A1154  ARG A1155  LEU A1162                    
SITE     2 AC4  7 TYR A1184  HOH A1409  HOH A1417                               
SITE     1 AC5  5 TRP A1143  TRP A1182  TYR A1189  6T4 A1306                    
SITE     2 AC5  5 HOH A1445                                                     
SITE     1 AC6  8 GLU A1141  ASN A1142  TRP A1143  SER A1175                    
SITE     2 AC6  8 ASP A1178  TYR A1189  ASN A1200  FMT A1305                    
SITE     1 AC7  5 TYR A1156  ILE A1157  HOH A1449  HOH A1469                    
SITE     2 AC7  5 HOH A1470                                                     
CRYST1   41.434   44.157   56.549  90.00  90.00  90.00 P 21 21 21    4          
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      0.024135  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.022646  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.017684        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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