HEADER HYDROLASE 04-AUG-15 5D1B TITLE CRYSTAL STRUCTURE OF G117E HDAC8 IN COMPLEX WITH TSA 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 MUTATION: 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHD2-XA-HIS KEYWDS HYDROLASE, HISTONE DEACETYLASE, ARGINASE/DEACETYLASE FOLD, ENZYME KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.DECROOS,N.H.CHRISTIANSON,L.E.GULLETT,C.M.BOWMAN,K.E.CHRISTIANSON, AUTHOR 2 M.A.DEARDORFF,D.W.CHRISTIANSON REVDAT 6 27-SEP-23 5D1B 1 LINK REVDAT 5 25-DEC-19 5D1B 1 REMARK REVDAT 4 13-SEP-17 5D1B 1 JRNL REMARK REVDAT 3 11-NOV-15 5D1B 1 JRNL REVDAT 2 28-OCT-15 5D1B 1 JRNL REVDAT 1 21-OCT-15 5D1B 0 JRNL AUTH C.DECROOS,N.H.CHRISTIANSON,L.E.GULLETT,C.M.BOWMAN, JRNL AUTH 2 K.E.CHRISTIANSON,M.A.DEARDORFF,D.W.CHRISTIANSON JRNL TITL BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF HDAC8 MUTANTS JRNL TITL 2 ASSOCIATED WITH CORNELIA DE LANGE SYNDROME SPECTRUM JRNL TITL 3 DISORDERS. JRNL REF BIOCHEMISTRY V. 54 6501 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 26463496 JRNL DOI 10.1021/ACS.BIOCHEM.5B00881 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1833 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 18247 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 934 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 49.7644 - 5.5393 1.00 2543 141 0.1593 0.1776 REMARK 3 2 5.5393 - 4.3975 1.00 2500 132 0.1640 0.2027 REMARK 3 3 4.3975 - 3.8419 1.00 2494 138 0.1668 0.2144 REMARK 3 4 3.8419 - 3.4907 1.00 2453 137 0.1956 0.2170 REMARK 3 5 3.4907 - 3.2406 1.00 2507 120 0.2277 0.2732 REMARK 3 6 3.2406 - 3.0496 1.00 2458 138 0.2489 0.2988 REMARK 3 7 3.0496 - 2.8968 0.96 2358 128 0.2765 0.3162 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.990 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 : 0.003 5711 REMARK 3 ANGLE : 0.627 7767 REMARK 3 CHIRALITY : 0.025 860 REMARK 3 PLANARITY : 0.003 994 REMARK 3 DIHEDRAL : 13.467 2011 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 5D1B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212502. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18263 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 49.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.46900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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 (%): 48.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BISTRIS (PH 6.5), 10% (W/V) PEG REMARK 280 35000, 4 MM TCEP, PH 7, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K 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 41.51550 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 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 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 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 ILE A 378 REMARK 465 GLU A 379 REMARK 465 GLY A 380 REMARK 465 ARG A 381 REMARK 465 GLY A 382 REMARK 465 SER A 383 REMARK 465 HIS A 384 REMARK 465 HIS A 385 REMARK 465 HIS A 386 REMARK 465 HIS A 387 REMARK 465 HIS A 388 REMARK 465 HIS A 389 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 379 REMARK 465 GLY B 380 REMARK 465 ARG B 381 REMARK 465 GLY B 382 REMARK 465 SER B 383 REMARK 465 HIS B 384 REMARK 465 HIS B 385 REMARK 465 HIS B 386 REMARK 465 HIS B 387 REMARK 465 HIS B 388 REMARK 465 HIS B 389 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 LYS A 60 CG CD CE NZ REMARK 470 GLU A 65 CG CD OE1 OE2 REMARK 470 ASP A 73 CG OD1 OD2 REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 GLU A 85 CG CD OE1 OE2 REMARK 470 LYS A 168 CE NZ REMARK 470 GLU A 238 CG CD OE1 OE2 REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 GLU A 250 CG CD OE1 OE2 REMARK 470 GLN A 293 CG CD OE1 NE2 REMARK 470 LYS A 325 CD CE NZ REMARK 470 GLU A 358 CG CD OE1 OE2 REMARK 470 HIS A 360 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 LYS A 374 CG CD CE NZ REMARK 470 ARG B 55 CZ NH1 NH2 REMARK 470 LYS B 60 CE NZ REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 GLN B 84 CG CD OE1 NE2 REMARK 470 ASP B 88 CG OD1 OD2 REMARK 470 ASP B 89 CG OD1 OD2 REMARK 470 ASP B 92 CG OD1 OD2 REMARK 470 SER B 93 OG REMARK 470 ILE B 94 CG1 CG2 CD1 REMARK 470 GLU B 106 CG CD OE1 OE2 REMARK 470 ASP B 110 CG OD1 OD2 REMARK 470 GLU B 117 CG CD OE1 OE2 REMARK 470 LYS B 221 CG CD CE NZ REMARK 470 GLU B 238 CG CD OE1 OE2 REMARK 470 LYS B 249 CE NZ REMARK 470 GLN B 253 CD OE1 NE2 REMARK 470 LYS B 325 CD CE NZ REMARK 470 LYS B 370 CE NZ REMARK 470 LYS B 374 CD CE NZ REMARK 470 VAL B 377 CG1 CG2 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 LYS A 36 10.88 58.96 REMARK 500 PHE A 70 -53.42 -128.70 REMARK 500 GLU A 85 -67.07 -152.09 REMARK 500 TYR A 100 -117.28 56.55 REMARK 500 PHE A 152 -5.00 70.97 REMARK 500 ASN A 256 71.91 49.28 REMARK 500 LEU A 264 56.34 -119.38 REMARK 500 SER A 276 -81.72 -107.86 REMARK 500 ASP B 147 21.11 -141.23 REMARK 500 ASN B 256 75.49 48.48 REMARK 500 LEU B 264 67.67 -116.05 REMARK 500 SER B 276 -71.87 -118.38 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 75.8 REMARK 620 3 ASP A 178 O 100.6 99.4 REMARK 620 4 HIS A 180 O 159.7 83.9 80.6 REMARK 620 5 SER A 199 OG 85.2 101.0 159.6 100.8 REMARK 620 6 LEU A 200 O 72.8 140.1 63.6 124.3 100.3 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 OD2 REMARK 620 2 HIS A 180 ND1 104.9 REMARK 620 3 ASP A 267 OD2 94.7 101.4 REMARK 620 4 TSN A 404 O2 158.0 90.0 98.2 REMARK 620 5 TSN A 404 O1 89.0 123.5 132.3 69.1 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 76.5 REMARK 620 3 VAL A 195 O 96.8 77.9 REMARK 620 4 TYR A 225 O 162.3 120.5 92.2 REMARK 620 N 1 2 3 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 79.4 REMARK 620 3 ASP B 178 O 111.0 102.2 REMARK 620 4 HIS B 180 O 156.3 76.9 75.3 REMARK 620 5 SER B 199 OG 88.6 96.6 154.8 93.2 REMARK 620 6 LEU B 200 O 80.0 150.6 66.4 122.4 103.6 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 OD2 REMARK 620 2 HIS B 180 ND1 116.0 REMARK 620 3 ASP B 267 OD2 95.4 108.8 REMARK 620 4 TSN B 404 O1 87.6 120.7 122.9 REMARK 620 5 TSN B 404 O2 153.0 84.7 93.7 66.2 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 71.6 REMARK 620 3 VAL B 195 O 99.7 83.0 REMARK 620 4 TYR B 225 O 165.6 121.1 89.0 REMARK 620 5 HOH B 501 O 82.7 88.0 169.3 90.7 REMARK 620 6 HOH B 502 O 70.8 142.0 109.0 95.7 81.7 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 TSN 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 TSN B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D1C RELATED DB: PDB REMARK 900 RELATED ID: 5D1D RELATED DB: PDB DBREF 5D1B A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 DBREF 5D1B B 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 SEQADV 5D1B GLU A 117 UNP Q9BY41 GLY 117 ENGINEERED MUTATION SEQADV 5D1B ILE A 378 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B GLU A 379 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B GLY A 380 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B ARG A 381 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B GLY A 382 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B SER A 383 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS A 384 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS A 385 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS A 386 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS A 387 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS A 388 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS A 389 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B GLU B 117 UNP Q9BY41 GLY 117 ENGINEERED MUTATION SEQADV 5D1B ILE B 378 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B GLU B 379 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B GLY B 380 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B ARG B 381 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B GLY B 382 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B SER B 383 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS B 384 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS B 385 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS B 386 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS B 387 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS B 388 UNP Q9BY41 EXPRESSION TAG SEQADV 5D1B HIS B 389 UNP Q9BY41 EXPRESSION TAG SEQRES 1 A 389 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 A 389 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 A 389 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 A 389 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 A 389 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 A 389 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 A 389 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 A 389 ASP SER ILE GLU TYR GLY LEU GLY TYR ASP CYS PRO ALA SEQRES 9 A 389 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLU SEQRES 10 A 389 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 A 389 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 A 389 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 A 389 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 A 389 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 A 389 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 A 389 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 A 389 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 A 389 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 A 389 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 A 389 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 A 389 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 A 389 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 A 389 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 A 389 ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 A 389 ARG CYS TRP THR TYR LEU THR GLY VAL ILE LEU GLY LYS SEQRES 26 A 389 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 A 389 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 A 389 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 A 389 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 30 A 389 ILE GLU GLY ARG GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 389 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 B 389 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 B 389 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 B 389 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 B 389 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 B 389 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 B 389 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 B 389 ASP SER ILE GLU TYR GLY LEU GLY TYR ASP CYS PRO ALA SEQRES 9 B 389 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLU SEQRES 10 B 389 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 B 389 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 B 389 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 B 389 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 B 389 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 B 389 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 B 389 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 B 389 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 B 389 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 B 389 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 B 389 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 B 389 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 B 389 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 B 389 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 B 389 ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 B 389 ARG CYS TRP THR TYR LEU THR GLY VAL ILE LEU GLY LYS SEQRES 26 B 389 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 B 389 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 B 389 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 B 389 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 30 B 389 ILE GLU GLY ARG GLY SER HIS HIS HIS HIS HIS HIS HET ZN A 401 1 HET K A 402 1 HET K A 403 1 HET TSN A 404 22 HET ZN B 401 1 HET K B 402 1 HET K B 403 1 HET TSN B 404 22 HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM TSN TRICHOSTATIN A HETSYN TSN 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7- HETSYN 2 TSN OXO-2,4-HEPTADIENAMIDE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 K 4(K 1+) FORMUL 6 TSN 2(C17 H22 N2 O3) FORMUL 11 HOH *17(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 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 THR A 280 GLN A 293 1 14 HELIX 12 AB3 ASN A 307 GLY A 324 1 18 HELIX 13 AB4 PHE A 336 GLY A 341 5 6 HELIX 14 AB5 GLU A 358 LYS A 374 1 17 HELIX 15 AB6 SER B 21 ASP B 29 1 9 HELIX 16 AB7 LYS B 36 TYR B 48 1 13 HELIX 17 AB8 ALA B 49 MET B 54 5 6 HELIX 18 AB9 SER B 63 ALA B 68 1 6 HELIX 19 AC1 THR B 72 GLY B 86 1 15 HELIX 20 AC2 GLY B 107 ASP B 128 1 22 HELIX 21 AC3 ASN B 156 ARG B 166 1 11 HELIX 22 AC4 GLY B 182 PHE B 189 1 8 HELIX 23 AC5 LEU B 219 ARG B 223 5 5 HELIX 24 AC6 GLN B 236 ASN B 256 1 21 HELIX 25 AC7 THR B 280 GLN B 293 1 14 HELIX 26 AC8 ASN B 307 GLY B 324 1 18 HELIX 27 AC9 PHE B 336 GLY B 341 5 6 HELIX 28 AD1 GLU B 358 LEU B 373 1 16 HELIX 29 AD2 LYS B 374 VAL B 376 5 3 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 ALA A 134 SHEET 5 AA1 8 ALA A 259 GLN A 263 1 N LEU A 262 O LEU A 301 SHEET 6 AA1 8 ILE A 172 ASP A 176 1 N LEU A 173 O VAL A 261 SHEET 7 AA1 8 VAL A 195 LYS A 202 1 O VAL A 198 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 VAL B 57 SHEET 3 AA2 8 VAL B 133 ASN B 136 1 O ILE B 135 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 LEU B 173 O VAL B 261 SHEET 7 AA2 8 VAL B 195 LYS B 202 1 O VAL B 198 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 2.88 LINK OD1 ASP A 176 K K A 402 1555 1555 2.69 LINK OD2 ASP A 178 ZN ZN A 401 1555 1555 2.03 LINK O ASP A 178 K K A 402 1555 1555 2.82 LINK ND1 HIS A 180 ZN ZN A 401 1555 1555 2.28 LINK O HIS A 180 K K A 402 1555 1555 2.85 LINK O PHE A 189 K K A 403 1555 1555 2.68 LINK O THR A 192 K K A 403 1555 1555 3.10 LINK O VAL A 195 K K A 403 1555 1555 2.75 LINK OG SER A 199 K K A 402 1555 1555 2.88 LINK O LEU A 200 K K A 402 1555 1555 2.79 LINK O TYR A 225 K K A 403 1555 1555 2.81 LINK OD2 ASP A 267 ZN ZN A 401 1555 1555 1.98 LINK ZN ZN A 401 O2 TSN A 404 1555 1555 2.22 LINK ZN ZN A 401 O1 TSN A 404 1555 1555 2.49 LINK O ASP B 176 K K B 402 1555 1555 2.80 LINK OD1 ASP B 176 K K B 402 1555 1555 2.62 LINK OD2 ASP B 178 ZN ZN B 401 1555 1555 2.00 LINK O ASP B 178 K K B 402 1555 1555 2.75 LINK ND1 HIS B 180 ZN ZN B 401 1555 1555 2.28 LINK O HIS B 180 K K B 402 1555 1555 3.11 LINK O PHE B 189 K K B 403 1555 1555 2.64 LINK O THR B 192 K K B 403 1555 1555 3.28 LINK O VAL B 195 K K B 403 1555 1555 2.74 LINK OG SER B 199 K K B 402 1555 1555 3.14 LINK O LEU B 200 K K B 402 1555 1555 2.78 LINK O TYR B 225 K K B 403 1555 1555 2.80 LINK OD2 ASP B 267 ZN ZN B 401 1555 1555 1.98 LINK ZN ZN B 401 O1 TSN B 404 1555 1555 2.64 LINK ZN ZN B 401 O2 TSN B 404 1555 1555 2.26 LINK K K B 403 O HOH B 501 1555 1555 2.95 LINK K K B 403 O HOH B 502 1555 1555 2.90 CISPEP 1 PHE A 208 PRO A 209 0 -1.24 CISPEP 2 GLY A 341 PRO A 342 0 0.25 CISPEP 3 PHE B 208 PRO B 209 0 -2.86 CISPEP 4 GLY B 341 PRO B 342 0 0.78 SITE 1 AC1 4 ASP A 178 HIS A 180 ASP A 267 TSN A 404 SITE 1 AC2 6 ASP A 176 ASP A 178 HIS A 180 SER A 199 SITE 2 AC2 6 LEU A 200 HIS A 201 SITE 1 AC3 4 PHE A 189 THR A 192 VAL A 195 TYR A 225 SITE 1 AC4 12 HIS A 142 HIS A 143 PHE A 152 ASP A 178 SITE 2 AC4 12 HIS A 180 ASP A 267 MET A 274 TYR A 306 SITE 3 AC4 12 ZN A 401 PRO B 273 MET B 274 TYR B 306 SITE 1 AC5 4 ASP B 178 HIS B 180 ASP B 267 TSN B 404 SITE 1 AC6 6 ASP B 176 ASP B 178 HIS B 180 SER B 199 SITE 2 AC6 6 LEU B 200 HIS B 201 SITE 1 AC7 7 PHE B 189 THR B 192 VAL B 195 TYR B 225 SITE 2 AC7 7 SER B 226 HOH B 501 HOH B 502 SITE 1 AC8 13 MET A 274 TYR A 306 TYR B 100 HIS B 142 SITE 2 AC8 13 HIS B 143 PHE B 152 ASP B 178 HIS B 180 SITE 3 AC8 13 PHE B 208 ASP B 267 MET B 274 TYR B 306 SITE 4 AC8 13 ZN B 401 CRYST1 52.197 83.031 98.460 90.00 102.77 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 0.019158 0.000000 0.004341 0.00000 SCALE2 0.000000 0.012044 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010414 0.00000