HEADER HYDROLASE 15-DEC-15 5FCW TITLE HDAC8 COMPLEXED WITH A HYDROXAMIC ACID 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 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 HISTONE DEACETYLASE, HDAC8, HYDROXAMIC ACID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.E.COLE,K.PERRY REVDAT 2 06-MAR-24 5FCW 1 JRNL REMARK LINK REVDAT 1 26-OCT-16 5FCW 0 JRNL AUTH A.A.TABACKMAN,R.FRANKSON,E.S.MARSAN,K.PERRY,K.E.COLE JRNL TITL STRUCTURE OF 'LINKERLESS' HYDROXAMIC ACID INHIBITOR-HDAC8 JRNL TITL 2 COMPLEX CONFIRMS THE FORMATION OF AN ISOFORM-SPECIFIC JRNL TITL 3 SUBPOCKET. JRNL REF J.STRUCT.BIOL. V. 195 373 2016 JRNL REFN ESSN 1095-8657 JRNL PMID 27374062 JRNL DOI 10.1016/J.JSB.2016.06.023 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 106016 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 5464 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 49.6744 - 6.1467 0.92 3304 161 0.1462 0.1615 REMARK 3 2 6.1467 - 4.8802 0.94 3407 154 0.1535 0.1497 REMARK 3 3 4.8802 - 4.2637 0.89 3208 179 0.1235 0.1399 REMARK 3 4 4.2637 - 3.8740 0.93 3297 181 0.1374 0.1535 REMARK 3 5 3.8740 - 3.5964 0.94 3359 167 0.1466 0.2276 REMARK 3 6 3.5964 - 3.3845 0.94 3424 162 0.1543 0.1899 REMARK 3 7 3.3845 - 3.2150 0.93 3314 197 0.1662 0.2179 REMARK 3 8 3.2150 - 3.0751 0.93 3345 172 0.1753 0.2343 REMARK 3 9 3.0751 - 2.9567 0.96 3408 188 0.1599 0.1995 REMARK 3 10 2.9567 - 2.8547 0.96 3456 166 0.1690 0.2226 REMARK 3 11 2.8547 - 2.7654 0.96 3440 199 0.1686 0.2656 REMARK 3 12 2.7654 - 2.6864 0.97 3502 181 0.1753 0.2065 REMARK 3 13 2.6864 - 2.6157 0.96 3446 194 0.1739 0.2544 REMARK 3 14 2.6157 - 2.5519 0.97 3431 195 0.1836 0.2552 REMARK 3 15 2.5519 - 2.4938 0.95 3444 184 0.1882 0.2660 REMARK 3 16 2.4938 - 2.4408 0.91 3275 158 0.1901 0.2696 REMARK 3 17 2.4408 - 2.3920 0.96 3423 196 0.1982 0.2454 REMARK 3 18 2.3920 - 2.3468 0.97 3488 198 0.1979 0.2379 REMARK 3 19 2.3468 - 2.3049 0.97 3421 183 0.2045 0.2760 REMARK 3 20 2.3049 - 2.2658 0.97 3507 190 0.2039 0.2618 REMARK 3 21 2.2658 - 2.2293 0.97 3395 168 0.2193 0.2234 REMARK 3 22 2.2293 - 2.1950 0.97 3517 211 0.2240 0.3001 REMARK 3 23 2.1950 - 2.1627 0.96 3448 188 0.2273 0.2746 REMARK 3 24 2.1627 - 2.1322 0.96 3410 174 0.2218 0.2898 REMARK 3 25 2.1322 - 2.1034 0.97 3535 194 0.2268 0.2573 REMARK 3 26 2.1034 - 2.0761 0.96 3371 208 0.2433 0.2986 REMARK 3 27 2.0761 - 2.0502 0.94 3348 166 0.2645 0.3252 REMARK 3 28 2.0502 - 2.0255 0.93 3387 190 0.2630 0.3185 REMARK 3 29 2.0255 - 2.0019 0.96 3411 176 0.2703 0.2736 REMARK 3 30 2.0019 - 1.9794 0.96 3398 184 0.2680 0.3104 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.410 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 : 0.007 5861 REMARK 3 ANGLE : 1.068 7955 REMARK 3 CHIRALITY : 0.070 860 REMARK 3 PLANARITY : 0.005 1012 REMARK 3 DIHEDRAL : 13.668 2132 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5FCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000214922. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI 11 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 107583 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 49.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% PEG 3350, 50 MM BUFFER (MES, PH REMARK 280 5.3), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 42.27400 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 ASP A 88 REMARK 465 HIS A 378 REMARK 465 HIS A 379 REMARK 465 HIS A 380 REMARK 465 HIS A 381 REMARK 465 HIS A 382 REMARK 465 HIS A 383 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 GLU B 85 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 HIS B 378 REMARK 465 HIS B 379 REMARK 465 HIS B 380 REMARK 465 HIS B 381 REMARK 465 HIS B 382 REMARK 465 HIS B 383 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 676 O HOH A 690 2.09 REMARK 500 OH TYR A 100 O HOH A 501 2.11 REMARK 500 O HOH B 606 O HOH B 635 2.12 REMARK 500 OH TYR A 306 O1 5YA A 401 2.15 REMARK 500 O HOH A 519 O HOH A 583 2.15 REMARK 500 OE1 GLU A 358 O HOH A 502 2.16 REMARK 500 O1 5YA B 401 O HOH B 501 2.17 REMARK 500 O HOH A 694 O HOH A 711 2.18 REMARK 500 NH1 ARG B 361 O HOH B 502 2.19 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 ILE A 34 77.42 -110.80 REMARK 500 GLU A 85 -168.97 -105.54 REMARK 500 TYR A 100 -97.21 -117.52 REMARK 500 GLU A 106 -112.94 -44.13 REMARK 500 SER A 276 -74.72 -114.58 REMARK 500 PHE B 70 -52.54 -123.33 REMARK 500 TYR B 100 -93.09 -110.74 REMARK 500 CYS B 102 77.43 -118.32 REMARK 500 PHE B 152 -2.20 73.85 REMARK 500 SER B 204 139.95 -170.80 REMARK 500 TYR B 224 1.07 82.24 REMARK 500 SER B 276 -75.61 -115.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 P6G A 404 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 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 O REMARK 620 2 ASP A 176 OD1 74.6 REMARK 620 3 ASP A 178 O 108.3 103.8 REMARK 620 4 HIS A 180 O 162.6 89.5 82.0 REMARK 620 5 SER A 199 OG 87.6 105.1 149.8 89.9 REMARK 620 6 LEU A 200 O 78.0 147.7 69.0 119.2 90.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 178 OD2 REMARK 620 2 HIS A 180 ND1 100.8 REMARK 620 3 ASP A 267 OD2 111.7 91.1 REMARK 620 4 5YA A 401 N1 110.8 82.3 137.5 REMARK 620 5 5YA A 401 O2 87.9 104.6 152.4 29.4 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 ASP B 176 O REMARK 620 2 ASP B 176 OD1 71.0 REMARK 620 3 ASP B 178 O 107.9 103.0 REMARK 620 4 HIS B 180 O 160.4 91.0 82.9 REMARK 620 5 SER B 199 OG 87.1 103.9 152.3 90.3 REMARK 620 6 LEU B 200 O 78.9 145.0 69.4 120.5 91.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 178 OD2 REMARK 620 2 HIS B 180 ND1 108.9 REMARK 620 3 ASP B 267 OD2 109.0 98.9 REMARK 620 4 5YA B 401 O2 139.3 108.3 80.9 REMARK 620 5 HOH B 501 O 87.1 104.0 146.0 68.2 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 5YA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN 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 P6G A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5YA B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN 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 5YA B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5YA B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 406 DBREF 5FCW A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 DBREF 5FCW B 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 SEQADV 5FCW HIS A 378 UNP Q9BY41 EXPRESSION TAG SEQADV 5FCW HIS A 379 UNP Q9BY41 EXPRESSION TAG SEQADV 5FCW HIS A 380 UNP Q9BY41 EXPRESSION TAG SEQADV 5FCW HIS A 381 UNP Q9BY41 EXPRESSION TAG SEQADV 5FCW HIS A 382 UNP Q9BY41 EXPRESSION TAG SEQADV 5FCW HIS A 383 UNP Q9BY41 EXPRESSION TAG SEQADV 5FCW HIS B 378 UNP Q9BY41 EXPRESSION TAG SEQADV 5FCW HIS B 379 UNP Q9BY41 EXPRESSION TAG SEQADV 5FCW HIS B 380 UNP Q9BY41 EXPRESSION TAG SEQADV 5FCW HIS B 381 UNP Q9BY41 EXPRESSION TAG SEQADV 5FCW HIS B 382 UNP Q9BY41 EXPRESSION TAG SEQADV 5FCW HIS B 383 UNP Q9BY41 EXPRESSION TAG SEQRES 1 A 383 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 A 383 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 A 383 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 A 383 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 A 383 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 A 383 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 A 383 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 A 383 ASP SER ILE GLU TYR GLY LEU GLY TYR ASP CYS PRO ALA SEQRES 9 A 383 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLY SEQRES 10 A 383 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 A 383 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 A 383 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 A 383 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 A 383 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 A 383 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 A 383 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 A 383 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 A 383 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 A 383 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 A 383 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 A 383 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 A 383 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 A 383 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 A 383 ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 A 383 ARG CYS TRP THR TYR LEU THR GLY VAL ILE LEU GLY LYS SEQRES 26 A 383 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 A 383 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 A 383 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 A 383 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 30 A 383 HIS HIS HIS HIS HIS HIS SEQRES 1 B 383 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 B 383 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 B 383 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 B 383 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 B 383 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 B 383 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 B 383 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 B 383 ASP SER ILE GLU TYR GLY LEU GLY TYR ASP CYS PRO ALA SEQRES 9 B 383 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLY SEQRES 10 B 383 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 B 383 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 B 383 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 B 383 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 B 383 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 B 383 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 B 383 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 B 383 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 B 383 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 B 383 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 B 383 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 B 383 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 B 383 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 B 383 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 B 383 ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 B 383 ARG CYS TRP THR TYR LEU THR GLY VAL ILE LEU GLY LYS SEQRES 26 B 383 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 B 383 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 B 383 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 B 383 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 30 B 383 HIS HIS HIS HIS HIS HIS HET 5YA A 401 20 HET ZN A 402 1 HET K A 403 1 HET P6G A 404 6 HET 5YA B 401 20 HET ZN B 402 1 HET K B 403 1 HET 5YA B 404 20 HET 5YA B 405 20 HET GOL B 406 6 HETNAM 5YA 4-NAPHTHALEN-1-YL-~{N}-OXIDANYL-BENZAMIDE HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM P6G HEXAETHYLENE GLYCOL HETNAM GOL GLYCEROL HETSYN P6G POLYETHYLENE GLYCOL PEG400 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 5YA 4(C17 H13 N O2) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 K 2(K 1+) FORMUL 6 P6G C12 H26 O7 FORMUL 12 GOL C3 H8 O3 FORMUL 13 HOH *414(H2 O) HELIX 1 AA1 SER A 21 SER A 30 1 10 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 GLU A 85 1 14 HELIX 6 AA6 SER A 93 GLY A 97 5 5 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 GLY A 324 1 18 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 LEU B 50 MET B 54 5 5 HELIX 19 AC1 SER B 63 ALA B 68 1 6 HELIX 20 AC2 THR B 72 SER B 83 1 12 HELIX 21 AC3 GLY B 107 ASP B 128 1 22 HELIX 22 AC4 ASN B 156 ARG B 166 1 11 HELIX 23 AC5 GLY B 182 SER B 190 1 9 HELIX 24 AC6 LEU B 219 ARG B 223 5 5 HELIX 25 AC7 GLN B 236 ASN B 256 1 21 HELIX 26 AC8 THR B 280 GLN B 293 1 14 HELIX 27 AC9 ASN B 307 GLY B 324 1 18 HELIX 28 AD1 PHE B 336 GLY B 341 5 6 HELIX 29 AD2 GLU B 358 HIS B 375 1 18 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 VAL A 17 SHEET 4 AA1 8 ALA A 297 LEU A 301 1 O ILE A 300 N ASN A 136 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 VAL A 261 SHEET 7 AA1 8 VAL A 195 LYS A 202 1 O VAL A 198 N ASP A 176 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 VAL B 133 N VAL B 17 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 VAL B 261 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 403 1555 1555 2.68 LINK OD1 ASP A 176 K K A 403 1555 1555 2.65 LINK OD2 ASP A 178 ZN ZN A 402 1555 1555 2.18 LINK O ASP A 178 K K A 403 1555 1555 2.68 LINK ND1 HIS A 180 ZN ZN A 402 1555 1555 2.26 LINK O HIS A 180 K K A 403 1555 1555 2.79 LINK OG SER A 199 K K A 403 1555 1555 2.86 LINK O LEU A 200 K K A 403 1555 1555 2.63 LINK OD2 ASP A 267 ZN ZN A 402 1555 1555 2.18 LINK N1 5YA A 401 ZN ZN A 402 1555 1555 2.62 LINK O2 5YA A 401 ZN ZN A 402 1555 1555 2.38 LINK O ASP B 176 K K B 403 1555 1555 2.73 LINK OD1 ASP B 176 K K B 403 1555 1555 2.72 LINK OD2 ASP B 178 ZN ZN B 402 1555 1555 2.15 LINK O ASP B 178 K K B 403 1555 1555 2.54 LINK ND1 HIS B 180 ZN ZN B 402 1555 1555 2.28 LINK O HIS B 180 K K B 403 1555 1555 2.72 LINK OG SER B 199 K K B 403 1555 1555 2.89 LINK O LEU B 200 K K B 403 1555 1555 2.64 LINK OD2 ASP B 267 ZN ZN B 402 1555 1555 2.11 LINK O2 5YA B 401 ZN ZN B 402 1555 1555 2.34 LINK ZN ZN B 402 O HOH B 501 1555 1555 2.39 CISPEP 1 PHE A 208 PRO A 209 0 -2.15 CISPEP 2 GLY A 341 PRO A 342 0 0.63 CISPEP 3 PHE B 208 PRO B 209 0 -2.84 CISPEP 4 GLY B 341 PRO B 342 0 2.31 SITE 1 AC1 12 ASP A 101 HIS A 142 HIS A 143 ASP A 178 SITE 2 AC1 12 HIS A 180 PHE A 208 ASP A 267 TYR A 306 SITE 3 AC1 12 ZN A 402 HOH A 655 PRO B 273 5YA B 405 SITE 1 AC2 4 ASP A 178 HIS A 180 ASP A 267 5YA A 401 SITE 1 AC3 5 ASP A 176 ASP A 178 HIS A 180 SER A 199 SITE 2 AC3 5 LEU A 200 SITE 1 AC4 1 GLU A 170 SITE 1 AC5 13 PRO A 273 TYR B 100 HIS B 143 GLY B 151 SITE 2 AC5 13 PHE B 152 HIS B 180 PHE B 208 ASP B 267 SITE 3 AC5 13 GLY B 304 TYR B 306 ZN B 402 5YA B 404 SITE 4 AC5 13 HOH B 501 SITE 1 AC6 5 ASP B 178 HIS B 180 ASP B 267 5YA B 401 SITE 2 AC6 5 HOH B 501 SITE 1 AC7 5 ASP B 176 ASP B 178 HIS B 180 SER B 199 SITE 2 AC7 5 LEU B 200 SITE 1 AC8 8 LYS A 33 PRO A 273 LYS B 33 TYR B 100 SITE 2 AC8 8 PRO B 273 MET B 274 5YA B 401 5YA B 405 SITE 1 AC9 8 TYR A 100 PHE A 152 5YA A 401 ALA B 32 SITE 2 AC9 8 LYS B 33 PHE B 152 TYR B 306 5YA B 404 SITE 1 AD1 3 ALA B 188 HOH B 517 HOH B 535 CRYST1 53.443 84.548 94.307 90.00 100.08 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 0.018712 0.000000 0.003327 0.00000 SCALE2 0.000000 0.011828 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010770 0.00000