HEADER HYDROLASE 25-JUN-04 1W22 TITLE CRYSTAL STRUCTURE OF INHIBITED HUMAN HDAC8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 8; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HDAC8, HD8, CDA07; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS HYDROXAMIC ACID, CHROMATIN, DEACETYLATION, HDAC, HYDROLASE, NUCLEAR KEYWDS 2 PROTEIN, REPRESSOR EXPDTA X-RAY DIFFRACTION AUTHOR A.VANNINI,C.VOLPARI,E.CAROLI CASAVOLA,S.DI MARCO REVDAT 5 13-DEC-23 1W22 1 REMARK LINK REVDAT 4 30-JAN-13 1W22 1 KEYWDS JRNL REMARK VERSN REVDAT 4 2 1 HETSYN FORMUL REVDAT 3 24-FEB-09 1W22 1 VERSN REVDAT 2 15-NOV-04 1W22 1 JRNL REVDAT 1 24-SEP-04 1W22 0 JRNL AUTH A.VANNINI,C.VOLPARI,G.FILOCAMO,E.CAROLI CASAVOLA,M.BRUNETTI, JRNL AUTH 2 D.RENZONI,P.CHAKRAVARTY,C.PAOLINI,R.DE FRANCESCO, JRNL AUTH 3 P.GALLINARI,C.STEINCKUHLER,S.DI MARCO JRNL TITL CRYSTAL STRUCTURE OF A EUKARYOTIC ZN-DEPENDENT HISTONE JRNL TITL 2 DEACETYLASE,HUMAN HDAC8,COMPLEXED WITH A HYDROXAMIC ACID JRNL TITL 3 INHIBITOR JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 15064 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 15477595 JRNL DOI 10.1073/PNAS.0404603101 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2002 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 27172 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1322 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 0.93 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5477 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01400 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : 0.50500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.05100 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.414 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.25 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.887 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.27 REMARK 3 BSOL : 36.55 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : L75_23JUNE.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : L75_23JUNE.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1W22 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1290020241. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9340 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27172 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1C3R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 41.76600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 PRO A 4 REMARK 465 GLU A 5 REMARK 465 GLU A 6 REMARK 465 PRO A 7 REMARK 465 ALA A 8 REMARK 465 ASP A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 GLN A 12 REMARK 465 GLU A 85 REMARK 465 GLY A 86 REMARK 465 ASP A 87 REMARK 465 ASP A 88 REMARK 465 ASP A 89 REMARK 465 HIS A 90 REMARK 465 PRO A 91 REMARK 465 ASP A 92 REMARK 465 SER A 93 REMARK 465 ILE A 94 REMARK 465 VAL A 376 REMARK 465 VAL A 377 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLU B 3 REMARK 465 PRO B 4 REMARK 465 GLU B 5 REMARK 465 GLU B 6 REMARK 465 PRO B 7 REMARK 465 ALA B 8 REMARK 465 ASP B 9 REMARK 465 SER B 10 REMARK 465 GLY B 11 REMARK 465 GLN B 12 REMARK 465 SER B 13 REMARK 465 LEU B 14 REMARK 465 GLY B 86 REMARK 465 ASP B 87 REMARK 465 ASP B 88 REMARK 465 ASP B 89 REMARK 465 HIS B 90 REMARK 465 PRO B 91 REMARK 465 ASP B 92 REMARK 465 SER B 93 REMARK 465 ILE B 94 REMARK 465 GLU B 95 REMARK 465 VAL B 376 REMARK 465 VAL B 377 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 SER A 13 N REMARK 470 HIS A 375 CA C O CB CG ND1 CD2 REMARK 470 HIS A 375 CE1 NE2 REMARK 470 HIS B 375 CA C O CB CG ND1 CD2 REMARK 470 HIS B 375 CE1 NE2 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 SER A 21 136.22 -170.43 REMARK 500 ILE A 34 49.80 -155.57 REMARK 500 LYS A 36 -3.26 66.77 REMARK 500 HIS A 51 -162.17 -63.25 REMARK 500 LYS A 52 16.19 50.52 REMARK 500 GLN A 53 -1.70 -140.99 REMARK 500 PHE A 70 -53.84 -135.06 REMARK 500 TYR A 100 -70.58 -64.07 REMARK 500 ALA A 104 78.21 -69.28 REMARK 500 MET A 130 52.38 38.41 REMARK 500 CYS A 131 113.72 174.23 REMARK 500 ASP A 147 34.36 -142.38 REMARK 500 GLU A 148 133.70 -170.11 REMARK 500 PRO A 205 -82.17 -23.44 REMARK 500 TYR A 224 3.02 81.06 REMARK 500 GLU A 238 -72.15 -50.56 REMARK 500 ASN A 256 75.22 -112.29 REMARK 500 SER A 276 -65.03 -123.99 REMARK 500 CYS A 352 31.79 -95.34 REMARK 500 ARG A 356 26.14 -70.32 REMARK 500 LYS A 374 68.28 -162.38 REMARK 500 SER B 21 139.06 -175.37 REMARK 500 ILE B 34 61.80 -158.08 REMARK 500 LYS B 36 -8.98 78.12 REMARK 500 HIS B 51 -165.44 -65.37 REMARK 500 LYS B 52 -6.92 55.33 REMARK 500 PHE B 70 -52.00 -133.83 REMARK 500 PRO B 103 170.09 -41.69 REMARK 500 ALA B 104 30.03 -92.69 REMARK 500 THR B 105 150.57 -47.44 REMARK 500 ASP B 128 -96.01 -53.82 REMARK 500 MET B 130 -67.06 -7.72 REMARK 500 ASN B 156 78.77 -102.40 REMARK 500 PRO B 205 -65.24 -23.19 REMARK 500 ASP B 233 153.24 -47.83 REMARK 500 ASN B 256 77.04 -116.32 REMARK 500 CYS B 275 56.61 32.00 REMARK 500 GLN B 293 21.71 -78.22 REMARK 500 ARG B 356 27.15 -78.58 REMARK 500 GLU B 358 90.03 63.00 REMARK 500 PRO B 359 -42.50 0.41 REMARK 500 HIS B 360 -70.33 -62.87 REMARK 500 ASN B 372 68.23 -58.20 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 A 340 0.06 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 A2019 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH B2010 DISTANCE = 7.29 ANGSTROMS REMARK 525 HOH B2046 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH B2056 DISTANCE = 7.50 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 K A1376 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 OD1 REMARK 620 2 ASP A 176 O 71.4 REMARK 620 3 ASP A 178 N 55.3 73.1 REMARK 620 4 ASP A 178 O 98.8 103.7 47.3 REMARK 620 5 HIS A 180 O 93.7 164.5 102.5 82.5 REMARK 620 6 SER A 199 OG 107.1 86.8 156.4 154.1 93.6 REMARK 620 7 LEU A 200 O 144.5 81.3 95.6 65.6 114.1 93.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1375 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 178 OD2 REMARK 620 2 HIS A 180 ND1 112.3 REMARK 620 3 ASP A 267 OD2 93.5 121.0 REMARK 620 4 NHB A1378 O26 70.4 106.5 132.4 REMARK 620 5 NHB A1378 O25 135.8 103.5 89.3 75.3 REMARK 620 6 NHB A1378 N24 100.9 88.1 139.4 31.4 54.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1377 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 189 O REMARK 620 2 THR A 192 O 66.9 REMARK 620 3 VAL A 195 O 115.4 77.4 REMARK 620 4 TYR A 225 O 158.5 125.5 85.7 REMARK 620 5 HOH A2074 O 77.0 143.7 117.1 89.9 REMARK 620 6 HOH A2093 O 78.8 89.4 153.6 83.6 86.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B1376 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 176 O REMARK 620 2 ASP B 176 OD1 73.0 REMARK 620 3 ASP B 178 N 72.9 56.7 REMARK 620 4 ASP B 178 O 106.5 99.7 48.8 REMARK 620 5 HIS B 180 O 156.0 84.8 102.6 85.7 REMARK 620 6 SER B 199 OG 83.3 104.7 153.0 155.5 93.9 REMARK 620 7 LEU B 200 O 76.1 140.6 91.2 66.5 127.9 95.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1375 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 178 OD2 REMARK 620 2 HIS B 180 ND1 110.0 REMARK 620 3 ASP B 267 OD2 106.4 111.8 REMARK 620 4 NHB B1378 N24 109.1 81.1 134.7 REMARK 620 5 NHB B1378 O25 148.2 91.9 85.1 50.3 REMARK 620 6 NHB B1378 O26 84.6 107.0 132.3 30.7 66.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B1377 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 189 O REMARK 620 2 THR B 192 O 70.4 REMARK 620 3 VAL B 195 O 104.0 74.8 REMARK 620 4 TYR B 225 O 169.8 118.3 84.1 REMARK 620 5 HOH B2060 O 77.7 148.0 112.9 93.6 REMARK 620 6 HOH B2063 O 87.6 91.9 157.7 86.9 88.0 REMARK 620 N 1 2 3 4 5 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. 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 1375 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1376 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1377 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1375 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 1376 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 1377 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHB A 1378 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHB B 1378 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T64 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH TRICHOSTATIN A REMARK 900 RELATED ID: 1T67 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH MS-344 REMARK 900 RELATED ID: 1T69 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH SAHA REMARK 900 RELATED ID: 1VKG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH CRA-19156 DBREF 1W22 A 1 377 UNP Q9BY41 HDA8_HUMAN 1 377 DBREF 1W22 B 1 377 UNP Q9BY41 HDA8_HUMAN 1 377 SEQRES 1 A 377 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 A 377 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 A 377 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 A 377 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 A 377 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 A 377 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 A 377 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 A 377 ASP SER ILE GLU TYR GLY LEU GLY TYR ASP CYS PRO ALA SEQRES 9 A 377 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLY SEQRES 10 A 377 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 A 377 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 A 377 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 A 377 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 A 377 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 A 377 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 A 377 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 A 377 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 A 377 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 A 377 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 A 377 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 A 377 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 A 377 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 A 377 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 A 377 ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 A 377 ARG CYS TRP THR TYR LEU THR GLY VAL ILE LEU GLY LYS SEQRES 26 A 377 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 A 377 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 A 377 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 A 377 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 1 B 377 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 B 377 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 B 377 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 B 377 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 B 377 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 B 377 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 B 377 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 B 377 ASP SER ILE GLU TYR GLY LEU GLY TYR ASP CYS PRO ALA SEQRES 9 B 377 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLY SEQRES 10 B 377 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 B 377 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 B 377 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 B 377 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 B 377 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 B 377 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 B 377 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 B 377 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 B 377 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 B 377 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 B 377 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 B 377 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 B 377 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 B 377 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 B 377 ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 B 377 ARG CYS TRP THR TYR LEU THR GLY VAL ILE LEU GLY LYS SEQRES 26 B 377 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 B 377 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 B 377 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 B 377 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL HET ZN A1375 1 HET K A1376 1 HET K A1377 1 HET NHB A1378 26 HET ZN B1375 1 HET K B1376 1 HET K B1377 1 HET NHB B1378 26 HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM NHB N-HYDROXY-4-(METHYL{[5-(2-PYRIDINYL)-2- HETNAM 2 NHB THIENYL]SULFONYL}AMINO)BENZAMIDE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 K 4(K 1+) FORMUL 6 NHB 2(C17 H15 N3 O4 S2) FORMUL 11 HOH *280(H2 O) HELIX 1 1 SER A 21 SER A 30 1 10 HELIX 2 2 LYS A 36 TYR A 48 1 13 HELIX 3 3 SER A 63 ALA A 68 1 6 HELIX 4 4 THR A 72 SER A 83 1 12 HELIX 5 5 GLY A 107 ASP A 128 1 22 HELIX 6 6 ASN A 156 ARG A 166 1 11 HELIX 7 7 GLY A 182 SER A 190 1 9 HELIX 8 8 GLN A 236 PHE A 255 1 20 HELIX 9 9 THR A 280 GLN A 293 1 14 HELIX 10 10 ASN A 307 GLY A 324 1 18 HELIX 11 11 GLU A 358 LEU A 373 1 16 HELIX 12 12 SER B 21 SER B 30 1 10 HELIX 13 13 LYS B 36 TYR B 48 1 13 HELIX 14 14 SER B 63 ALA B 68 1 6 HELIX 15 15 THR B 72 GLU B 85 1 14 HELIX 16 16 GLY B 107 GLY B 129 1 23 HELIX 17 17 ASN B 156 ARG B 166 1 11 HELIX 18 18 GLY B 182 SER B 190 1 9 HELIX 19 19 GLN B 236 PHE B 255 1 20 HELIX 20 20 THR B 280 GLN B 293 1 14 HELIX 21 21 ASN B 307 LEU B 323 1 17 HELIX 22 22 PRO B 359 ASN B 372 1 14 SHEET 1 AA 8 ARG A 55 VAL A 57 0 SHEET 2 AA 8 VAL A 17 ILE A 19 1 O TYR A 18 N VAL A 57 SHEET 3 AA 8 VAL A 133 ASN A 136 1 O VAL A 133 N VAL A 17 SHEET 4 AA 8 ALA A 297 LEU A 301 1 O THR A 298 N ALA A 134 SHEET 5 AA 8 ALA A 259 GLN A 263 1 O VAL A 260 N LEU A 299 SHEET 6 AA 8 ILE A 172 ASP A 176 1 O LEU A 173 N VAL A 261 SHEET 7 AA 8 VAL A 195 LYS A 202 1 O MET A 196 N TYR A 174 SHEET 8 AA 8 SER A 226 ILE A 231 1 O VAL A 227 N SER A 199 SHEET 1 BA 8 ARG B 55 VAL B 57 0 SHEET 2 BA 8 VAL B 17 ILE B 19 1 O TYR B 18 N VAL B 57 SHEET 3 BA 8 VAL B 133 ASN B 136 1 O VAL B 133 N VAL B 17 SHEET 4 BA 8 ALA B 297 LEU B 301 1 O THR B 298 N ALA B 134 SHEET 5 BA 8 ALA B 259 GLN B 263 1 O VAL B 260 N LEU B 299 SHEET 6 BA 8 ILE B 172 ASP B 176 1 O LEU B 173 N VAL B 261 SHEET 7 BA 8 VAL B 195 LYS B 202 1 O MET B 196 N TYR B 174 SHEET 8 BA 8 SER B 226 ILE B 231 1 O VAL B 227 N SER B 199 LINK OD1 ASP A 176 K K A1376 1555 1555 3.01 LINK O ASP A 176 K K A1376 1555 1555 3.05 LINK OD2 ASP A 178 ZN ZN A1375 1555 1555 2.05 LINK N ASP A 178 K K A1376 1555 1555 3.45 LINK O ASP A 178 K K A1376 1555 1555 2.92 LINK ND1 HIS A 180 ZN ZN A1375 1555 1555 2.01 LINK O HIS A 180 K K A1376 1555 1555 2.81 LINK O PHE A 189 K K A1377 1555 1555 2.89 LINK O THR A 192 K K A1377 1555 1555 3.05 LINK O VAL A 195 K K A1377 1555 1555 2.76 LINK OG SER A 199 K K A1376 1555 1555 3.12 LINK O LEU A 200 K K A1376 1555 1555 2.89 LINK O TYR A 225 K K A1377 1555 1555 3.09 LINK OD2 ASP A 267 ZN ZN A1375 1555 1555 2.00 LINK ZN ZN A1375 O26 NHB A1378 1555 1555 2.16 LINK ZN ZN A1375 O25 NHB A1378 1555 1555 2.17 LINK ZN ZN A1375 N24 NHB A1378 1555 1555 2.60 LINK K K A1377 O HOH A2074 1555 1555 3.05 LINK K K A1377 O HOH A2093 1555 1555 3.05 LINK O ASP B 176 K K B1376 1555 1555 2.92 LINK OD1 ASP B 176 K K B1376 1555 1555 3.04 LINK OD2 ASP B 178 ZN ZN B1375 1555 1555 2.03 LINK N ASP B 178 K K B1376 1555 1555 3.41 LINK O ASP B 178 K K B1376 1555 1555 2.84 LINK ND1 HIS B 180 ZN ZN B1375 1555 1555 2.05 LINK O HIS B 180 K K B1376 1555 1555 2.94 LINK O PHE B 189 K K B1377 1555 1555 2.82 LINK O THR B 192 K K B1377 1555 1555 3.19 LINK O VAL B 195 K K B1377 1555 1555 2.88 LINK OG SER B 199 K K B1376 1555 1555 3.02 LINK O LEU B 200 K K B1376 1555 1555 2.95 LINK O TYR B 225 K K B1377 1555 1555 3.22 LINK OD2 ASP B 267 ZN ZN B1375 1555 1555 2.04 LINK ZN ZN B1375 N24 NHB B1378 1555 1555 2.65 LINK ZN ZN B1375 O25 NHB B1378 1555 1555 2.50 LINK ZN ZN B1375 O26 NHB B1378 1555 1555 2.14 LINK K K B1377 O HOH B2060 1555 1555 3.08 LINK K K B1377 O HOH B2063 1555 1555 3.23 CISPEP 1 PHE A 208 PRO A 209 0 -0.32 CISPEP 2 PHE B 208 PRO B 209 0 0.32 SITE 1 AC1 4 ASP A 178 HIS A 180 ASP A 267 NHB A1378 SITE 1 AC2 5 ASP A 176 ASP A 178 HIS A 180 SER A 199 SITE 2 AC2 5 LEU A 200 SITE 1 AC3 6 PHE A 189 THR A 192 VAL A 195 TYR A 225 SITE 2 AC3 6 HOH A2074 HOH A2093 SITE 1 AC4 4 ASP B 178 HIS B 180 ASP B 267 NHB B1378 SITE 1 AC5 6 ASP B 176 ASP B 178 HIS B 180 SER B 199 SITE 2 AC5 6 LEU B 200 HIS B 201 SITE 1 AC6 5 PHE B 189 THR B 192 VAL B 195 TYR B 225 SITE 2 AC6 5 HOH B2060 SITE 1 AC7 17 ASP A 101 HIS A 142 HIS A 143 GLY A 151 SITE 2 AC7 17 PHE A 152 ASP A 178 HIS A 180 PHE A 208 SITE 3 AC7 17 ASP A 267 GLY A 304 TYR A 306 ZN A1375 SITE 4 AC7 17 HOH A2009 HOH A2154 LYS B 33 PRO B 273 SITE 5 AC7 17 TYR B 306 SITE 1 AC8 15 LYS A 33 PHE A 152 PRO A 273 ASP B 101 SITE 2 AC8 15 HIS B 142 HIS B 143 GLY B 151 PHE B 152 SITE 3 AC8 15 ASP B 178 HIS B 180 PHE B 208 ASP B 267 SITE 4 AC8 15 TYR B 306 ZN B1375 HOH B2058 CRYST1 51.746 83.532 94.653 90.00 97.48 90.00 P 1 21 1 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 0.019325 0.000000 0.002537 0.00000 SCALE2 0.000000 0.011971 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010656 0.00000