HEADER HYDROLASE 01-OCT-18 6HSK TITLE CRYSTAL STRUCTURE OF A HUMAN HDAC8 L6 LOOP MUTANT COMPLEXED WITH TITLE 2 QUISINOSTAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 8; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HD8; COMPND 5 EC: 3.5.1.98; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: HUMAN HDAC8 WITH LOOP L6 (AGDPMCS) REPLACED BY HUMAN COMPND 8 HDAC1 LOOP L6 (SGDRLGC) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HDAC8, HDACL1, CDA07; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EPIGENETICS, HISTONE DEACETYLASE, HDAC8, SELECTIVE INHIBITOR, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.MAREK,T.B.SHAIK,E.RAMOS-MORALES,C.ROMIER REVDAT 5 24-JAN-24 6HSK 1 LINK REVDAT 4 28-NOV-18 6HSK 1 JRNL REVDAT 3 14-NOV-18 6HSK 1 TITLE REVDAT 2 07-NOV-18 6HSK 1 JRNL REVDAT 1 31-OCT-18 6HSK 0 JRNL AUTH M.MAREK,T.B.SHAIK,T.HEIMBURG,A.CHAKRABARTI,J.LANCELOT, JRNL AUTH 2 E.RAMOS-MORALES,C.DA VEIGA,D.KALININ,J.MELESINA,D.ROBAA, JRNL AUTH 3 K.SCHMIDTKUNZ,T.SUZUKI,R.HOLL,E.ENNIFAR,R.J.PIERCE,M.JUNG, JRNL AUTH 4 W.SIPPL,C.ROMIER JRNL TITL CHARACTERIZATION OF HISTONE DEACETYLASE 8 (HDAC8) SELECTIVE JRNL TITL 2 INHIBITION REVEALS SPECIFIC ACTIVE SITE STRUCTURAL AND JRNL TITL 3 FUNCTIONAL DETERMINANTS. JRNL REF J. MED. CHEM. V. 61 10000 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30347148 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01087 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.930 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 60780 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3039 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 37.4761 - 5.8651 1.00 2618 138 0.1322 0.1437 REMARK 3 2 5.8651 - 4.6581 1.00 2626 138 0.1355 0.1523 REMARK 3 3 4.6581 - 4.0701 1.00 2623 139 0.1113 0.1450 REMARK 3 4 4.0701 - 3.6983 1.00 2657 139 0.1216 0.1528 REMARK 3 5 3.6983 - 3.4334 1.00 2607 138 0.1312 0.1594 REMARK 3 6 3.4334 - 3.2311 1.00 2653 139 0.1407 0.1745 REMARK 3 7 3.2311 - 3.0694 1.00 2643 140 0.1565 0.2166 REMARK 3 8 3.0694 - 2.9358 1.00 2633 138 0.1482 0.1901 REMARK 3 9 2.9358 - 2.8228 1.00 2645 138 0.1575 0.2043 REMARK 3 10 2.8228 - 2.7255 1.00 2627 139 0.1559 0.2187 REMARK 3 11 2.7255 - 2.6403 1.00 2634 138 0.1584 0.2012 REMARK 3 12 2.6403 - 2.5648 1.00 2638 139 0.1599 0.2174 REMARK 3 13 2.5648 - 2.4973 1.00 2622 138 0.1755 0.2275 REMARK 3 14 2.4973 - 2.4364 1.00 2641 139 0.1826 0.2518 REMARK 3 15 2.4364 - 2.3810 1.00 2635 139 0.1804 0.2099 REMARK 3 16 2.3810 - 2.3304 1.00 2621 138 0.1945 0.2502 REMARK 3 17 2.3304 - 2.2837 1.00 2636 139 0.2027 0.2578 REMARK 3 18 2.2837 - 2.2407 1.00 2624 138 0.2173 0.2536 REMARK 3 19 2.2407 - 2.2006 1.00 2625 138 0.2377 0.2650 REMARK 3 20 2.2006 - 2.1633 1.00 2632 139 0.2523 0.3197 REMARK 3 21 2.1633 - 2.1284 1.00 2625 138 0.2686 0.3243 REMARK 3 22 2.1284 - 2.0957 0.93 2476 130 0.2962 0.3374 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 5902 REMARK 3 ANGLE : 0.868 8012 REMARK 3 CHIRALITY : 0.054 869 REMARK 3 PLANARITY : 0.005 1068 REMARK 3 DIHEDRAL : 16.326 3506 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -16.0716 10.6717 -1.2960 REMARK 3 T TENSOR REMARK 3 T11: 0.2359 T22: 0.2523 REMARK 3 T33: 0.2119 T12: 0.0242 REMARK 3 T13: -0.0083 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 1.3353 L22: 0.7652 REMARK 3 L33: 0.5796 L12: -0.2141 REMARK 3 L13: 0.2782 L23: -0.0227 REMARK 3 S TENSOR REMARK 3 S11: -0.0339 S12: -0.0909 S13: -0.0209 REMARK 3 S21: 0.0615 S22: 0.0445 S23: -0.0204 REMARK 3 S31: -0.0637 S32: -0.0791 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -34.3692 27.4284 -39.4361 REMARK 3 T TENSOR REMARK 3 T11: 0.1768 T22: 0.2264 REMARK 3 T33: 0.1946 T12: 0.0367 REMARK 3 T13: 0.0106 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.8590 L22: 0.6303 REMARK 3 L33: 0.6731 L12: -0.3117 REMARK 3 L13: 0.2731 L23: -0.2126 REMARK 3 S TENSOR REMARK 3 S11: -0.0038 S12: -0.0534 S13: 0.0160 REMARK 3 S21: -0.0586 S22: -0.0280 S23: -0.0956 REMARK 3 S31: -0.0069 S32: 0.0070 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HSK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1200012183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60783 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.096 REMARK 200 RESOLUTION RANGE LOW (A) : 46.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.15980 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 1.21300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.080 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1T67 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS TRIS PROPANE PH 7.5, 0.2 M REMARK 280 NANO3, 17-21% PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 54.68667 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 27.34333 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 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 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 SER A 13 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 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 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 O HOH A 662 O HOH A 680 2.11 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 CYS A 276 -61.72 -94.73 REMARK 500 TYR B 224 3.77 82.01 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 A 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 O REMARK 620 2 ASP A 176 OD1 73.1 REMARK 620 3 ASP A 178 O 109.7 104.3 REMARK 620 4 HIS A 180 O 158.7 86.9 81.8 REMARK 620 5 SER A 199 OG 85.5 101.4 152.9 91.5 REMARK 620 6 LEU A 200 O 81.4 149.7 69.1 119.9 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 178 OD1 REMARK 620 2 HIS A 180 ND1 100.3 REMARK 620 3 ASP A 267 OD2 103.0 96.9 REMARK 620 4 GOK A 404 O3 167.2 84.0 88.4 REMARK 620 5 GOK A 404 O4 92.0 93.7 159.7 75.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 189 O REMARK 620 2 THR A 192 O 82.0 REMARK 620 3 VAL A 195 O 120.3 84.6 REMARK 620 4 TYR A 225 O 153.4 116.7 82.1 REMARK 620 5 HOH A 512 O 90.7 95.3 148.5 69.8 REMARK 620 6 HOH A 611 O 75.2 156.9 109.7 84.0 81.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 176 O REMARK 620 2 ASP B 176 OD1 71.6 REMARK 620 3 ASP B 178 O 108.0 106.3 REMARK 620 4 HIS B 180 O 160.2 89.9 83.3 REMARK 620 5 SER B 199 OG 85.5 102.4 150.9 92.0 REMARK 620 6 LEU B 200 O 79.5 147.3 68.2 120.2 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 178 OD1 REMARK 620 2 HIS B 180 ND1 98.7 REMARK 620 3 ASP B 267 OD2 106.4 92.9 REMARK 620 4 GOK B 404 O3 166.8 86.8 85.2 REMARK 620 5 GOK B 404 O4 92.5 98.4 156.3 74.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 189 O REMARK 620 2 THR B 192 O 83.5 REMARK 620 3 VAL B 195 O 116.6 85.5 REMARK 620 4 TYR B 225 O 152.9 118.9 82.2 REMARK 620 5 HOH B 518 O 94.7 95.4 148.5 69.8 REMARK 620 6 HOH B 621 O 76.5 159.2 108.4 79.1 80.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOK A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOK B 404 DBREF 6HSK A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 DBREF 6HSK B 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 SEQADV 6HSK GLY A -2 UNP Q9BY41 EXPRESSION TAG SEQADV 6HSK SER A -1 UNP Q9BY41 EXPRESSION TAG SEQADV 6HSK HIS A 0 UNP Q9BY41 EXPRESSION TAG SEQADV 6HSK SER A 270 UNP Q9BY41 ALA 270 CONFLICT SEQADV 6HSK ARG A 273 UNP Q9BY41 PRO 273 CONFLICT SEQADV 6HSK LEU A 274 UNP Q9BY41 MET 274 CONFLICT SEQADV 6HSK GLY A 275 UNP Q9BY41 CYS 275 CONFLICT SEQADV 6HSK CYS A 276 UNP Q9BY41 SER 276 CONFLICT SEQADV 6HSK GLY B -2 UNP Q9BY41 EXPRESSION TAG SEQADV 6HSK SER B -1 UNP Q9BY41 EXPRESSION TAG SEQADV 6HSK HIS B 0 UNP Q9BY41 EXPRESSION TAG SEQADV 6HSK SER B 270 UNP Q9BY41 ALA 270 CONFLICT SEQADV 6HSK ARG B 273 UNP Q9BY41 PRO 273 CONFLICT SEQADV 6HSK LEU B 274 UNP Q9BY41 MET 274 CONFLICT SEQADV 6HSK GLY B 275 UNP Q9BY41 CYS 275 CONFLICT SEQADV 6HSK CYS B 276 UNP Q9BY41 SER 276 CONFLICT SEQRES 1 A 380 GLY SER HIS MET GLU GLU PRO GLU GLU PRO ALA ASP SER SEQRES 2 A 380 GLY GLN SER LEU VAL PRO VAL TYR ILE TYR SER PRO GLU SEQRES 3 A 380 TYR VAL SER MET CYS ASP SER LEU ALA LYS ILE PRO LYS SEQRES 4 A 380 ARG ALA SER MET VAL HIS SER LEU ILE GLU ALA TYR ALA SEQRES 5 A 380 LEU HIS LYS GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SEQRES 6 A 380 SER MET GLU GLU MET ALA THR PHE HIS THR ASP ALA TYR SEQRES 7 A 380 LEU GLN HIS LEU GLN LYS VAL SER GLN GLU GLY ASP ASP SEQRES 8 A 380 ASP HIS PRO ASP SER ILE GLU TYR GLY LEU GLY TYR ASP SEQRES 9 A 380 CYS PRO ALA THR GLU GLY ILE PHE ASP TYR ALA ALA ALA SEQRES 10 A 380 ILE GLY GLY ALA THR ILE THR ALA ALA GLN CYS LEU ILE SEQRES 11 A 380 ASP GLY MET CYS LYS VAL ALA ILE ASN TRP SER GLY GLY SEQRES 12 A 380 TRP HIS HIS ALA LYS LYS ASP GLU ALA SER GLY PHE CYS SEQRES 13 A 380 TYR LEU ASN ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG SEQRES 14 A 380 ARG LYS PHE GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU SEQRES 15 A 380 HIS HIS GLY ASP GLY VAL GLU ASP ALA PHE SER PHE THR SEQRES 16 A 380 SER LYS VAL MET THR VAL SER LEU HIS LYS PHE SER PRO SEQRES 17 A 380 GLY PHE PHE PRO GLY THR GLY ASP VAL SER ASP VAL GLY SEQRES 18 A 380 LEU GLY LYS GLY ARG TYR TYR SER VAL ASN VAL PRO ILE SEQRES 19 A 380 GLN ASP GLY ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS SEQRES 20 A 380 GLU SER VAL LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO SEQRES 21 A 380 LYS ALA VAL VAL LEU GLN LEU GLY ALA ASP THR ILE SER SEQRES 22 A 380 GLY ASP ARG LEU GLY CYS PHE ASN MET THR PRO VAL GLY SEQRES 23 A 380 ILE GLY LYS CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU SEQRES 24 A 380 ALA THR LEU ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA SEQRES 25 A 380 ASN THR ALA ARG CYS TRP THR TYR LEU THR GLY VAL ILE SEQRES 26 A 380 LEU GLY LYS THR LEU SER SER GLU ILE PRO ASP HIS GLU SEQRES 27 A 380 PHE PHE THR ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE SEQRES 28 A 380 THR PRO SER CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG SEQRES 29 A 380 ILE GLN GLN ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS SEQRES 30 A 380 HIS VAL VAL SEQRES 1 B 380 GLY SER HIS MET GLU GLU PRO GLU GLU PRO ALA ASP SER SEQRES 2 B 380 GLY GLN SER LEU VAL PRO VAL TYR ILE TYR SER PRO GLU SEQRES 3 B 380 TYR VAL SER MET CYS ASP SER LEU ALA LYS ILE PRO LYS SEQRES 4 B 380 ARG ALA SER MET VAL HIS SER LEU ILE GLU ALA TYR ALA SEQRES 5 B 380 LEU HIS LYS GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SEQRES 6 B 380 SER MET GLU GLU MET ALA THR PHE HIS THR ASP ALA TYR SEQRES 7 B 380 LEU GLN HIS LEU GLN LYS VAL SER GLN GLU GLY ASP ASP SEQRES 8 B 380 ASP HIS PRO ASP SER ILE GLU TYR GLY LEU GLY TYR ASP SEQRES 9 B 380 CYS PRO ALA THR GLU GLY ILE PHE ASP TYR ALA ALA ALA SEQRES 10 B 380 ILE GLY GLY ALA THR ILE THR ALA ALA GLN CYS LEU ILE SEQRES 11 B 380 ASP GLY MET CYS LYS VAL ALA ILE ASN TRP SER GLY GLY SEQRES 12 B 380 TRP HIS HIS ALA LYS LYS ASP GLU ALA SER GLY PHE CYS SEQRES 13 B 380 TYR LEU ASN ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG SEQRES 14 B 380 ARG LYS PHE GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU SEQRES 15 B 380 HIS HIS GLY ASP GLY VAL GLU ASP ALA PHE SER PHE THR SEQRES 16 B 380 SER LYS VAL MET THR VAL SER LEU HIS LYS PHE SER PRO SEQRES 17 B 380 GLY PHE PHE PRO GLY THR GLY ASP VAL SER ASP VAL GLY SEQRES 18 B 380 LEU GLY LYS GLY ARG TYR TYR SER VAL ASN VAL PRO ILE SEQRES 19 B 380 GLN ASP GLY ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS SEQRES 20 B 380 GLU SER VAL LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO SEQRES 21 B 380 LYS ALA VAL VAL LEU GLN LEU GLY ALA ASP THR ILE SER SEQRES 22 B 380 GLY ASP ARG LEU GLY CYS PHE ASN MET THR PRO VAL GLY SEQRES 23 B 380 ILE GLY LYS CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU SEQRES 24 B 380 ALA THR LEU ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA SEQRES 25 B 380 ASN THR ALA ARG CYS TRP THR TYR LEU THR GLY VAL ILE SEQRES 26 B 380 LEU GLY LYS THR LEU SER SER GLU ILE PRO ASP HIS GLU SEQRES 27 B 380 PHE PHE THR ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE SEQRES 28 B 380 THR PRO SER CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG SEQRES 29 B 380 ILE GLN GLN ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS SEQRES 30 B 380 HIS VAL VAL HET ZN A 401 1 HET K A 402 1 HET K A 403 1 HET GOK A 404 29 HET ZN B 401 1 HET K B 402 1 HET K B 403 1 HET GOK B 404 29 HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM GOK 2-[4-[[(1-METHYLINDOL-3-YL) HETNAM 2 GOK METHYLAMINO]METHYL]PIPERIDIN-1-YL]-~{N}-OXIDANYL- HETNAM 3 GOK PYRIMIDINE-5-CARBOXAMIDE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 K 4(K 1+) FORMUL 6 GOK 2(C21 H26 N6 O2) FORMUL 11 HOH *461(H2 O) HELIX 1 AA1 SER A 21 ASP A 29 1 9 HELIX 2 AA2 LYS A 36 TYR A 48 1 13 HELIX 3 AA3 ALA A 49 MET A 54 5 6 HELIX 4 AA4 SER A 63 ALA A 68 1 6 HELIX 5 AA5 THR A 72 GLN A 84 1 13 HELIX 6 AA6 HIS A 90 GLY A 97 5 8 HELIX 7 AA7 GLY A 107 ASP A 128 1 22 HELIX 8 AA8 ASN A 156 ARG A 166 1 11 HELIX 9 AA9 GLY A 182 PHE A 189 1 8 HELIX 10 AB1 LEU A 219 ARG A 223 5 5 HELIX 11 AB2 GLN A 236 ASN A 256 1 21 HELIX 12 AB3 THR A 280 GLN A 293 1 14 HELIX 13 AB4 ASN A 307 LEU A 323 1 17 HELIX 14 AB5 PHE A 336 GLY A 341 5 6 HELIX 15 AB6 GLU A 358 HIS A 375 1 18 HELIX 16 AB7 SER B 21 SER B 30 1 10 HELIX 17 AB8 LYS B 36 TYR B 48 1 13 HELIX 18 AB9 ALA B 49 MET B 54 5 6 HELIX 19 AC1 SER B 63 ALA B 68 1 6 HELIX 20 AC2 THR B 72 GLN B 84 1 13 HELIX 21 AC3 HIS B 90 GLY B 97 5 8 HELIX 22 AC4 GLY B 107 ASP B 128 1 22 HELIX 23 AC5 ASN B 156 ARG B 166 1 11 HELIX 24 AC6 GLY B 182 PHE B 189 1 8 HELIX 25 AC7 LEU B 219 ARG B 223 5 5 HELIX 26 AC8 GLN B 236 ASN B 256 1 21 HELIX 27 AC9 GLY B 265 ILE B 269 5 5 HELIX 28 AD1 THR B 280 GLN B 293 1 14 HELIX 29 AD2 ASN B 307 LEU B 323 1 17 HELIX 30 AD3 PHE B 336 GLY B 341 5 6 HELIX 31 AD4 GLU B 358 LYS B 374 1 17 SHEET 1 AA1 8 ARG A 55 VAL A 57 0 SHEET 2 AA1 8 VAL A 17 ILE A 19 1 N TYR A 18 O ARG A 55 SHEET 3 AA1 8 VAL A 133 ASN A 136 1 O ILE A 135 N ILE A 19 SHEET 4 AA1 8 ALA A 297 LEU A 301 1 O ILE A 300 N ALA A 134 SHEET 5 AA1 8 ALA A 259 GLN A 263 1 N LEU A 262 O LEU A 299 SHEET 6 AA1 8 ILE A 172 ASP A 176 1 N VAL A 175 O GLN A 263 SHEET 7 AA1 8 VAL A 195 LYS A 202 1 O MET A 196 N TYR A 174 SHEET 8 AA1 8 SER A 226 ILE A 231 1 O VAL A 227 N THR A 197 SHEET 1 AA2 8 ARG B 55 VAL B 57 0 SHEET 2 AA2 8 VAL B 17 ILE B 19 1 N TYR B 18 O ARG B 55 SHEET 3 AA2 8 VAL B 133 ASN B 136 1 O ILE B 135 N ILE B 19 SHEET 4 AA2 8 ALA B 297 LEU B 301 1 O ILE B 300 N ALA B 134 SHEET 5 AA2 8 ALA B 259 GLN B 263 1 N LEU B 262 O LEU B 299 SHEET 6 AA2 8 ILE B 172 ASP B 176 1 N VAL B 175 O GLN B 263 SHEET 7 AA2 8 VAL B 195 LYS B 202 1 O MET B 196 N TYR B 174 SHEET 8 AA2 8 SER B 226 ILE B 231 1 O VAL B 227 N THR B 197 LINK O ASP A 176 K K A 402 1555 1555 2.74 LINK OD1 ASP A 176 K K A 402 1555 1555 2.70 LINK OD1 ASP A 178 ZN ZN A 401 1555 1555 2.05 LINK O ASP A 178 K K A 402 1555 1555 2.68 LINK ND1 HIS A 180 ZN ZN A 401 1555 1555 2.22 LINK O HIS A 180 K K A 402 1555 1555 2.77 LINK O PHE A 189 K K A 403 1555 1555 2.52 LINK O THR A 192 K K A 403 1555 1555 2.66 LINK O VAL A 195 K K A 403 1555 1555 2.41 LINK OG SER A 199 K K A 402 1555 1555 2.93 LINK O LEU A 200 K K A 402 1555 1555 2.61 LINK O TYR A 225 K K A 403 1555 1555 3.21 LINK OD2 ASP A 267 ZN ZN A 401 1555 1555 2.01 LINK ZN ZN A 401 O3 GOK A 404 1555 1555 2.27 LINK ZN ZN A 401 O4 GOK A 404 1555 1555 2.13 LINK K K A 403 O HOH A 512 1555 1555 2.60 LINK K K A 403 O HOH A 611 1555 1555 2.79 LINK O ASP B 176 K K B 402 1555 1555 2.82 LINK OD1 ASP B 176 K K B 402 1555 1555 2.62 LINK OD1 ASP B 178 ZN ZN B 401 1555 1555 2.07 LINK O ASP B 178 K K B 402 1555 1555 2.66 LINK ND1 HIS B 180 ZN ZN B 401 1555 1555 2.23 LINK O HIS B 180 K K B 402 1555 1555 2.74 LINK O PHE B 189 K K B 403 1555 1555 2.44 LINK O THR B 192 K K B 403 1555 1555 2.68 LINK O VAL B 195 K K B 403 1555 1555 2.46 LINK OG SER B 199 K K B 402 1555 1555 2.91 LINK O LEU B 200 K K B 402 1555 1555 2.62 LINK O TYR B 225 K K B 403 1555 1555 3.27 LINK OD2 ASP B 267 ZN ZN B 401 1555 1555 2.06 LINK ZN ZN B 401 O3 GOK B 404 1555 1555 2.35 LINK ZN ZN B 401 O4 GOK B 404 1555 1555 2.13 LINK K K B 403 O HOH B 518 1555 1555 2.51 LINK K K B 403 O HOH B 621 1555 1555 2.72 CISPEP 1 PHE A 208 PRO A 209 0 -0.81 CISPEP 2 GLY A 341 PRO A 342 0 3.03 CISPEP 3 PHE B 208 PRO B 209 0 -1.88 CISPEP 4 GLY B 341 PRO B 342 0 1.62 SITE 1 AC1 4 ASP A 178 HIS A 180 ASP A 267 GOK A 404 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 A 512 HOH A 611 SITE 1 AC4 14 HIS A 142 HIS A 143 GLY A 151 PHE A 152 SITE 2 AC4 14 ARG A 167 ASP A 178 HIS A 180 GLY A 206 SITE 3 AC4 14 PHE A 208 PRO A 209 ASP A 267 TYR A 306 SITE 4 AC4 14 ZN A 401 HOH A 629 SITE 1 AC5 4 ASP B 178 HIS B 180 ASP B 267 GOK B 404 SITE 1 AC6 5 ASP B 176 ASP B 178 HIS B 180 SER B 199 SITE 2 AC6 5 LEU B 200 SITE 1 AC7 6 PHE B 189 THR B 192 VAL B 195 TYR B 225 SITE 2 AC7 6 HOH B 518 HOH B 621 SITE 1 AC8 16 HIS B 142 HIS B 143 GLY B 151 PHE B 152 SITE 2 AC8 16 ARG B 167 ASP B 178 HIS B 180 GLY B 206 SITE 3 AC8 16 PHE B 208 PRO B 209 ASP B 267 TYR B 306 SITE 4 AC8 16 ZN B 401 HOH B 502 HOH B 646 HOH B 672 CRYST1 106.390 106.390 82.030 90.00 90.00 120.00 P 32 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 0.009399 0.005427 0.000000 0.00000 SCALE2 0.000000 0.010853 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012191 0.00000