HEADER HYDROLASE/HYDROLASE INHIBITOR 14-APR-17 5VI6 TITLE CRYSTAL STRUCTURE OF HISTONE DEACETYLASE 8 IN COMPLEX WITH TRAPOXIN A COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 8; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 8-377; COMPND 5 SYNONYM: HD8; COMPND 6 EC: 3.5.1.98; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TRAPOXIN A; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: (3S,6S,9S,15AR)-6,9-DIBENZYL-3-{6,6-DIHYDROXY-6-[(2S)- COMPND 12 OXIRAN-2-YL]HEXYL}OCTAHYDRO-2H-PYRIDO[1,2-A][1,4,7, COMPND 13 10]TETRAAZACYCLODODECINE-1,4,7,10(3H,12H)-TETRONE; COMPND 14 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; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HELICOMA AMBIENS; SOURCE 11 ORGANISM_COMMON: ASCOMYCETES; SOURCE 12 ORGANISM_TAXID: 314151 KEYWDS HDAC, EPIGENETICS, NATURAL PRODUCT INHIBITOR, HYDROLASE, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.J.PORTER,D.W.CHRISTIANSON REVDAT 6 15-NOV-23 5VI6 1 LINK ATOM REVDAT 5 04-OCT-23 5VI6 1 LINK REVDAT 4 01-JAN-20 5VI6 1 REMARK REVDAT 3 27-SEP-17 5VI6 1 JRNL REVDAT 2 13-SEP-17 5VI6 1 HEADER COMPND SOURCE KEYWDS REVDAT 2 2 1 REMARK DBREF SEQRES HET REVDAT 2 3 1 HETNAM HETSYN FORMUL LINK REVDAT 2 4 1 SITE ATOM REVDAT 1 06-SEP-17 5VI6 0 JRNL AUTH N.J.PORTER,D.W.CHRISTIANSON JRNL TITL BINDING OF THE MICROBIAL CYCLIC TETRAPEPTIDE TRAPOXIN A TO JRNL TITL 2 THE CLASS I HISTONE DEACETYLASE HDAC8. JRNL REF ACS CHEM. BIOL. V. 12 2281 2017 JRNL REFN ESSN 1554-8937 JRNL PMID 28846375 JRNL DOI 10.1021/ACSCHEMBIO.7B00330 REMARK 2 REMARK 2 RESOLUTION. 1.24 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 95812 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.122 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 4939 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 41.3085 - 3.8426 1.00 3022 178 0.1341 0.1444 REMARK 3 2 3.8426 - 3.0503 1.00 3082 155 0.1260 0.1249 REMARK 3 3 3.0503 - 2.6648 0.98 2990 158 0.1245 0.1442 REMARK 3 4 2.6648 - 2.4212 1.00 3055 160 0.1164 0.1386 REMARK 3 5 2.4212 - 2.2477 1.00 3074 160 0.1077 0.1267 REMARK 3 6 2.2477 - 2.1152 1.00 2985 202 0.1107 0.1373 REMARK 3 7 2.1152 - 2.0092 1.00 3114 140 0.1066 0.1398 REMARK 3 8 2.0092 - 1.9218 0.96 2902 197 0.1073 0.1174 REMARK 3 9 1.9218 - 1.8478 0.99 3034 150 0.1024 0.1170 REMARK 3 10 1.8478 - 1.7840 1.00 3060 140 0.1032 0.1369 REMARK 3 11 1.7840 - 1.7282 1.00 3095 150 0.0968 0.1372 REMARK 3 12 1.7282 - 1.6788 1.00 3074 142 0.0951 0.1192 REMARK 3 13 1.6788 - 1.6346 1.00 3026 179 0.0942 0.1272 REMARK 3 14 1.6346 - 1.5948 1.00 3058 170 0.0984 0.1335 REMARK 3 15 1.5948 - 1.5585 0.94 2886 176 0.1018 0.1524 REMARK 3 16 1.5585 - 1.5253 0.97 3013 122 0.0999 0.1258 REMARK 3 17 1.5253 - 1.4948 0.99 2993 170 0.1004 0.1249 REMARK 3 18 1.4948 - 1.4666 0.99 3052 176 0.1075 0.1434 REMARK 3 19 1.4666 - 1.4404 1.00 3063 150 0.1212 0.1505 REMARK 3 20 1.4404 - 1.4160 1.00 3001 164 0.1315 0.1671 REMARK 3 21 1.4160 - 1.3932 1.00 3082 182 0.1355 0.1925 REMARK 3 22 1.3932 - 1.3717 1.00 3031 178 0.1395 0.1799 REMARK 3 23 1.3717 - 1.3515 0.98 3027 159 0.1498 0.1854 REMARK 3 24 1.3515 - 1.3325 0.95 2937 155 0.1597 0.1820 REMARK 3 25 1.3325 - 1.3145 0.99 2947 202 0.1631 0.2028 REMARK 3 26 1.3145 - 1.2974 1.00 3046 160 0.1802 0.1940 REMARK 3 27 1.2974 - 1.2812 1.00 3008 196 0.1883 0.2250 REMARK 3 28 1.2812 - 1.2658 1.00 3123 170 0.1940 0.2507 REMARK 3 29 1.2658 - 1.2510 1.00 3045 136 0.2118 0.2606 REMARK 3 30 1.2510 - 1.2370 1.00 3048 162 0.2223 0.2474 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.230 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 : 0.009 3099 REMARK 3 ANGLE : 1.033 4215 REMARK 3 CHIRALITY : 0.081 451 REMARK 3 PLANARITY : 0.008 550 REMARK 3 DIHEDRAL : 22.330 1130 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 5VI6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227460. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95873 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.237 REMARK 200 RESOLUTION RANGE LOW (A) : 44.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 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: 3EWF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% DIOXANE, PH 8.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K 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 77.67800 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 38.83900 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE TRAPOXIN A IS CYCLIC PEPTIDE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: TRAPOXIN A REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 SER A 6 REMARK 465 ASN 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 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 HIS A 375 REMARK 465 VAL A 376 REMARK 465 VAL A 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 LEU A 14 CG CD1 CD2 REMARK 470 VAL A 15 CG1 CG2 REMARK 470 LYS A 58 CD CE NZ REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 GLU A 106 CD OE1 OE2 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 HH TYR A 18 HD1 HIS A 42 1.14 REMARK 500 HD21 ASN A 136 O HOH A 512 1.56 REMARK 500 HZ1 LYS A 36 O HOH A 509 1.56 REMARK 500 O2 EDO A 412 O HOH A 502 2.02 REMARK 500 O HOH A 656 O HOH A 806 2.16 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 52.86 -142.77 REMARK 500 TYR A 100 -96.34 -104.17 REMARK 500 GLU A 148 118.05 -164.00 REMARK 500 PHE A 152 -1.51 75.86 REMARK 500 TYR A 224 2.23 81.77 REMARK 500 SER A 276 -73.23 -121.47 REMARK 500 SER A 276 -73.23 -122.56 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 73.0 REMARK 620 3 ASP A 178 O 107.9 104.3 REMARK 620 4 HIS A 180 O 160.5 88.6 82.3 REMARK 620 5 SER A 199 OG 85.2 101.9 153.1 92.8 REMARK 620 6 LEU A 200 O 78.6 147.4 69.5 120.8 91.1 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 OD2 REMARK 620 2 HIS A 180 ND1 105.2 REMARK 620 3 ASP A 267 OD2 112.1 97.9 REMARK 620 4 5OM B 4 O01 125.6 113.3 99.4 REMARK 620 5 5OM B 4 O02 86.5 87.2 158.3 59.6 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 78.7 REMARK 620 3 VAL A 195 O 114.7 82.3 REMARK 620 4 TYR A 225 O 156.3 121.0 83.1 REMARK 620 5 HOH A 590 O 90.0 97.0 154.4 75.3 REMARK 620 6 HOH A 730 O 72.8 151.4 111.9 86.3 80.7 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 EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DIO A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DIO A 415 DBREF 5VI6 A 8 377 UNP Q9BY41 HDAC8_HUMAN 8 377 DBREF 5VI6 B 1 4 PDB 5VI6 5VI6 1 4 SEQADV 5VI6 SER A 6 UNP Q9BY41 EXPRESSION TAG SEQADV 5VI6 ASN A 7 UNP Q9BY41 EXPRESSION TAG SEQRES 1 A 372 SER ASN ALA ASP SER GLY GLN SER LEU VAL PRO VAL TYR SEQRES 2 A 372 ILE TYR SER PRO GLU TYR VAL SER MET CYS ASP SER LEU SEQRES 3 A 372 ALA LYS ILE PRO LYS ARG ALA SER MET VAL HIS SER LEU SEQRES 4 A 372 ILE GLU ALA TYR ALA LEU HIS LYS GLN MET ARG ILE VAL SEQRES 5 A 372 LYS PRO LYS VAL ALA SER MET GLU GLU MET ALA THR PHE SEQRES 6 A 372 HIS THR ASP ALA TYR LEU GLN HIS LEU GLN LYS VAL SER SEQRES 7 A 372 GLN GLU GLY ASP ASP ASP HIS PRO ASP SER ILE GLU TYR SEQRES 8 A 372 GLY LEU GLY TYR ASP CYS PRO ALA THR GLU GLY ILE PHE SEQRES 9 A 372 ASP TYR ALA ALA ALA ILE GLY GLY ALA THR ILE THR ALA SEQRES 10 A 372 ALA GLN CYS LEU ILE ASP GLY MET CYS LYS VAL ALA ILE SEQRES 11 A 372 ASN TRP SER GLY GLY TRP HIS HIS ALA LYS LYS ASP GLU SEQRES 12 A 372 ALA SER GLY PHE CYS TYR LEU ASN ASP ALA VAL LEU GLY SEQRES 13 A 372 ILE LEU ARG LEU ARG ARG LYS PHE GLU ARG ILE LEU TYR SEQRES 14 A 372 VAL ASP LEU ASP LEU HIS HIS GLY ASP GLY VAL GLU ASP SEQRES 15 A 372 ALA PHE SER PHE THR SER LYS VAL MET THR VAL SER LEU SEQRES 16 A 372 HIS LYS PHE SER PRO GLY PHE PHE PRO GLY THR GLY ASP SEQRES 17 A 372 VAL SER ASP VAL GLY LEU GLY LYS GLY ARG TYR TYR SER SEQRES 18 A 372 VAL ASN VAL PRO ILE GLN ASP GLY ILE GLN ASP GLU LYS SEQRES 19 A 372 TYR TYR GLN ILE CYS GLU SER VAL LEU LYS GLU VAL TYR SEQRES 20 A 372 GLN ALA PHE ASN PRO LYS ALA VAL VAL LEU GLN LEU GLY SEQRES 21 A 372 ALA ASP THR ILE ALA GLY ASP PRO MET CYS SER PHE ASN SEQRES 22 A 372 MET THR PRO VAL GLY ILE GLY LYS CYS LEU LYS TYR ILE SEQRES 23 A 372 LEU GLN TRP GLN LEU ALA THR LEU ILE LEU GLY GLY GLY SEQRES 24 A 372 GLY TYR ASN LEU ALA ASN THR ALA ARG CYS TRP THR TYR SEQRES 25 A 372 LEU THR GLY VAL ILE LEU GLY LYS THR LEU SER SER GLU SEQRES 26 A 372 ILE PRO ASP HIS GLU PHE PHE THR ALA TYR GLY PRO ASP SEQRES 27 A 372 TYR VAL LEU GLU ILE THR PRO SER CYS ARG PRO ASP ARG SEQRES 28 A 372 ASN GLU PRO HIS ARG ILE GLN GLN ILE LEU ASN TYR ILE SEQRES 29 A 372 LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 1 B 4 PHE PHE CPI 5OM HET CPI B 3 17 HET 5OM B 4 32 HET ZN A 401 1 HET K A 402 1 HET K A 403 1 HET EDO A 404 10 HET EDO A 405 10 HET EDO A 406 10 HET EDO A 407 10 HET EDO A 408 20 HET EDO A 409 20 HET EDO A 410 10 HET EDO A 411 10 HET EDO A 412 10 HET EDO A 413 10 HET DIO A 414 14 HET DIO A 415 14 HETNAM CPI 6-CARBOXYPIPERIDINE HETNAM 5OM (2S)-2-AMINO-8,8-DIHYDROXY-8-[(2S)-OXIRAN-2-YL]OCTANOIC HETNAM 2 5OM ACID HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM DIO 1,4-DIETHYLENE DIOXIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CPI C6 H11 N O2 FORMUL 2 5OM C10 H19 N O5 FORMUL 3 ZN ZN 2+ FORMUL 4 K 2(K 1+) FORMUL 6 EDO 10(C2 H6 O2) FORMUL 16 DIO 2(C4 H8 O2) FORMUL 18 HOH *377(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 GLU A 85 1 14 HELIX 6 AA6 GLY A 107 ASP A 128 1 22 HELIX 7 AA7 ASN A 156 ARG A 166 1 11 HELIX 8 AA8 GLY A 182 PHE A 189 1 8 HELIX 9 AA9 LEU A 219 ARG A 223 5 5 HELIX 10 AB1 GLN A 236 ASN A 256 1 21 HELIX 11 AB2 GLY A 265 ILE A 269 5 5 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 LEU A 373 1 16 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 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 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 LINK N PHE B 1 C 5OM B 4 1555 1555 1.37 LINK C PHE B 2 N CPI B 3 1555 1555 1.41 LINK C CPI B 3 N 5OM B 4 1555 1555 1.37 LINK O ASP A 176 K K A 402 1555 1555 2.78 LINK OD1 ASP A 176 K K A 402 1555 1555 2.68 LINK OD2 ASP A 178 ZN ZN A 401 1555 1555 1.96 LINK O ASP A 178 K K A 402 1555 1555 2.68 LINK ND1 HIS A 180 ZN ZN A 401 1555 1555 2.07 LINK O HIS A 180 K K A 402 1555 1555 2.76 LINK O PHE A 189 K K A 403 1555 1555 2.61 LINK O THR A 192 K K A 403 1555 1555 2.85 LINK O VAL A 195 K K A 403 1555 1555 2.59 LINK OG SER A 199 K K A 402 1555 1555 2.88 LINK O LEU A 200 K K A 402 1555 1555 2.65 LINK O TYR A 225 K K A 403 1555 1555 2.99 LINK OD2 ASP A 267 ZN ZN A 401 1555 1555 1.97 LINK ZN ZN A 401 O01 5OM B 4 1555 1555 1.93 LINK ZN ZN A 401 O02 5OM B 4 1555 1555 2.49 LINK K K A 403 O HOH A 590 1555 1555 2.75 LINK K K A 403 O HOH A 730 1555 1555 2.78 CISPEP 1 PHE A 208 PRO A 209 0 -1.25 CISPEP 2 GLY A 341 PRO A 342 0 4.06 CISPEP 3 PHE B 2 CPI B 3 0 5.87 SITE 1 AC1 4 ASP A 178 HIS A 180 ASP A 267 5OM B 4 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 590 HOH A 730 SITE 1 AC4 5 SER A 63 MET A 64 ASP A 355 HOH A 616 SITE 2 AC4 5 HOH A 686 SITE 1 AC5 3 ARG A 166 ARG A 167 GLU A 170 SITE 1 AC6 5 GLU A 23 TYR A 24 ALA A 114 HOH A 601 SITE 2 AC6 5 HOH A 631 SITE 1 AC7 1 MET A 274 SITE 1 AC8 9 PRO A 281 VAL A 282 ARG A 313 TYR A 317 SITE 2 AC8 9 LEU A 346 GLU A 347 ILE A 348 HOH A 531 SITE 3 AC8 9 HOH A 604 SITE 1 AC9 5 GLY A 206 PHE A 207 PHE A 208 PRO A 209 SITE 2 AC9 5 GLY A 210 SITE 1 AD1 8 HIS A 143 LYS A 145 SER A 150 ASP A 183 SITE 2 AD1 8 PHE A 208 PRO A 209 HOH A 548 HOH A 632 SITE 1 AD2 6 TYR A 111 TRP A 141 PHE A 152 CYS A 153 SITE 2 AD2 6 TYR A 154 LEU A 155 SITE 1 AD3 9 CYS A 28 ILE A 34 ARG A 37 ALA A 38 SITE 2 AD3 9 SER A 138 HOH A 502 HOH A 505 HOH A 519 SITE 3 AD3 9 HOH A 657 SITE 1 AD4 3 ARG A 361 GLN A 364 TYR A 368 SITE 1 AD5 6 TYR A 224 TYR A 225 ALA A 254 ASN A 372 SITE 2 AD5 6 LEU A 373 HOH A 681 SITE 1 AD6 4 THR A 69 LEU A 163 ALA A 188 PHE A 189 CRYST1 50.980 50.980 116.517 90.00 90.00 120.00 P 32 3 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 0.019616 0.011325 0.000000 0.00000 SCALE2 0.000000 0.022650 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008582 0.00000