HEADER HYDROLASE 23-AUG-15 5DC7 TITLE CRYSTAL STRUCTURE OF D176A-Y306F HDAC8 IN COMPLEX WITH A TETRAPEPTIDE TITLE 2 SUBSTRATE 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; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: FLUOR-DE-LYS TETRAPEPTIDE ASSAY SUBSTRATE; COMPND 10 CHAIN: C, D; COMPND 11 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHD2-XA-HIS; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS HISTONE DEACETYLASE 8, ARGINASE FOLD, DEACETYLASE, ENZYME-SUBSTRATE KEYWDS 2 COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.DECROOS,M.S.LEE,D.W.CHRISTIANSON REVDAT 6 15-NOV-23 5DC7 1 LINK REVDAT 5 27-SEP-23 5DC7 1 LINK REVDAT 4 25-DEC-19 5DC7 1 REMARK REVDAT 3 13-SEP-17 5DC7 1 JRNL REMARK REVDAT 2 17-FEB-16 5DC7 1 JRNL REVDAT 1 03-FEB-16 5DC7 0 JRNL AUTH S.M.GANTT,C.DECROOS,M.S.LEE,L.E.GULLETT,C.M.BOWMAN, JRNL AUTH 2 D.W.CHRISTIANSON,C.A.FIERKE JRNL TITL GENERAL BASE-GENERAL ACID CATALYSIS IN HUMAN HISTONE JRNL TITL 2 DEACETYLASE 8. JRNL REF BIOCHEMISTRY V. 55 820 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 26806311 JRNL DOI 10.1021/ACS.BIOCHEM.5B01327 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 37384 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1872 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 44.2116 - 5.3989 1.00 2946 151 0.1557 0.1729 REMARK 3 2 5.3989 - 4.2864 1.00 2808 151 0.1414 0.1895 REMARK 3 3 4.2864 - 3.7449 1.00 2776 136 0.1339 0.1550 REMARK 3 4 3.7449 - 3.4026 1.00 2769 140 0.1533 0.1899 REMARK 3 5 3.4026 - 3.1588 0.99 2728 141 0.1724 0.2279 REMARK 3 6 3.1588 - 2.9726 0.99 2715 155 0.1786 0.2393 REMARK 3 7 2.9726 - 2.8238 0.99 2694 159 0.1890 0.2516 REMARK 3 8 2.8238 - 2.7009 0.99 2696 142 0.2005 0.2713 REMARK 3 9 2.7009 - 2.5969 0.99 2707 141 0.1983 0.2402 REMARK 3 10 2.5969 - 2.5073 0.99 2701 130 0.2094 0.2838 REMARK 3 11 2.5073 - 2.4289 0.99 2696 143 0.2191 0.2784 REMARK 3 12 2.4289 - 2.3595 0.99 2644 149 0.2347 0.3307 REMARK 3 13 2.3595 - 2.3000 0.96 2632 134 0.2606 0.3428 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) : 22.070 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 5897 REMARK 3 ANGLE : 0.732 8008 REMARK 3 CHIRALITY : 0.027 872 REMARK 3 PLANARITY : 0.003 1024 REMARK 3 DIHEDRAL : 12.886 2092 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 5DC7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-14 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 : 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 : 37434 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 44.203 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.90600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 47.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS (PH 8.0), 15% (W/V) PEG REMARK 280 10000, AND 4 MM TCEP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 40.92250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.80800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.87400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.80800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.92250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.87400 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 VAL A 377 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 ILE B 378 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 SER A 13 OG REMARK 470 LEU A 14 CG CD1 CD2 REMARK 470 LYS A 36 CE NZ REMARK 470 ARG A 55 NE CZ NH1 NH2 REMARK 470 LYS A 60 CD CE NZ REMARK 470 LYS A 81 CD CE NZ REMARK 470 GLU A 85 CD OE1 OE2 REMARK 470 ASP A 89 CG OD1 OD2 REMARK 470 LYS A 132 CD CE NZ REMARK 470 ARG A 223 CZ NH1 NH2 REMARK 470 GLU A 238 CD OE1 OE2 REMARK 470 LYS A 249 CD CE NZ REMARK 470 GLN A 253 CD OE1 NE2 REMARK 470 GLN A 295 CD OE1 NE2 REMARK 470 GLU A 330 CD OE1 OE2 REMARK 470 LYS A 374 CE NZ REMARK 470 LYS B 52 CE NZ REMARK 470 ARG B 55 CZ NH1 NH2 REMARK 470 LYS B 58 CE NZ REMARK 470 LYS B 60 CG CD CE NZ REMARK 470 GLU B 65 CD OE1 OE2 REMARK 470 ASP B 73 CG OD1 OD2 REMARK 470 GLU B 85 CG CD OE1 OE2 REMARK 470 ASP B 89 CG OD1 OD2 REMARK 470 GLU B 106 CG CD OE1 OE2 REMARK 470 LYS B 132 CD CE NZ REMARK 470 LYS B 168 CD CE NZ REMARK 470 LYS B 221 CD CE NZ REMARK 470 ARG B 223 CZ NH1 NH2 REMARK 470 GLN B 253 CD OE1 NE2 REMARK 470 GLU B 335 CD OE1 OE2 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 ASP A 87 85.62 -68.31 REMARK 500 ASP A 88 43.08 -95.59 REMARK 500 LEU A 264 59.86 -118.48 REMARK 500 SER A 276 -70.30 -111.38 REMARK 500 CYS A 352 59.35 -100.24 REMARK 500 ILE B 34 55.39 -140.46 REMARK 500 PHE B 70 -44.86 -133.16 REMARK 500 ASP B 89 25.42 -143.88 REMARK 500 ASN B 256 71.50 45.05 REMARK 500 SER B 276 -73.51 -113.96 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 178 OD2 REMARK 620 2 HIS A 180 ND1 114.1 REMARK 620 3 ASP A 267 OD2 99.7 114.3 REMARK 620 4 ALY C 5 OH 122.4 114.0 87.7 REMARK 620 N 1 2 3 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 PHE A 189 O REMARK 620 2 THR A 192 O 74.0 REMARK 620 3 VAL A 195 O 111.3 83.5 REMARK 620 4 TYR A 225 O 159.6 122.2 84.4 REMARK 620 5 HOH A 510 O 87.3 95.3 160.0 79.4 REMARK 620 6 HOH A 561 O 70.6 144.4 112.2 91.8 80.1 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 110.4 REMARK 620 3 ASP B 267 OD2 103.4 106.0 REMARK 620 4 ALY D 5 OH 120.4 114.9 99.4 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 PHE B 189 O REMARK 620 2 THR B 192 O 76.8 REMARK 620 3 VAL B 195 O 110.8 82.0 REMARK 620 4 TYR B 225 O 159.7 119.5 84.9 REMARK 620 5 HOH B 521 O 84.5 96.9 163.8 81.5 REMARK 620 6 HOH B 538 O 71.4 147.6 114.9 90.5 74.2 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 GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DC5 RELATED DB: PDB REMARK 900 RELATED ID: 5DC6 RELATED DB: PDB REMARK 900 RELATED ID: 5DC8 RELATED DB: PDB DBREF 5DC7 A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 DBREF 5DC7 B 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 DBREF 5DC7 C 1 6 PDB 5DC7 5DC7 1 6 DBREF 5DC7 D 1 6 PDB 5DC7 5DC7 1 6 SEQADV 5DC7 ALA A 176 UNP Q9BY41 ASP 176 ENGINEERED MUTATION SEQADV 5DC7 PHE A 306 UNP Q9BY41 TYR 306 ENGINEERED MUTATION SEQADV 5DC7 ILE A 378 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 GLU A 379 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 GLY A 380 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 ARG A 381 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 GLY A 382 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 SER A 383 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 HIS A 384 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 HIS A 385 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 HIS A 386 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 HIS A 387 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 HIS A 388 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 HIS A 389 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 ALA B 176 UNP Q9BY41 ASP 176 ENGINEERED MUTATION SEQADV 5DC7 PHE B 306 UNP Q9BY41 TYR 306 ENGINEERED MUTATION SEQADV 5DC7 ILE B 378 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 GLU B 379 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 GLY B 380 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 ARG B 381 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 GLY B 382 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 SER B 383 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 HIS B 384 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 HIS B 385 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 HIS B 386 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 HIS B 387 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 HIS B 388 UNP Q9BY41 EXPRESSION TAG SEQADV 5DC7 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 GLY 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 ALA 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 PHE 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 GLY 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 ALA 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 PHE 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 SEQRES 1 C 6 ACE ARG HIS ALY ALY MCM SEQRES 1 D 6 ACE ARG HIS ALY ALY MCM HET ACE C 1 3 HET ALY C 4 12 HET ALY C 5 12 HET MCM C 6 13 HET ACE D 1 3 HET ALY D 4 12 HET ALY D 5 12 HET MCM D 6 13 HET ZN A 401 1 HET K A 402 1 HET GOL A 403 6 HET ZN B 401 1 HET K B 402 1 HET GOL B 403 6 HET GOL B 404 6 HET GOL D 101 6 HETNAM ACE ACETYL GROUP HETNAM ALY N(6)-ACETYLLYSINE HETNAM MCM 7-AMINO-4-METHYL-CHROMEN-2-ONE HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETSYN MCM 7-AMINO-4-METHYLCOUMARIN HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ACE 2(C2 H4 O) FORMUL 3 ALY 4(C8 H16 N2 O3) FORMUL 3 MCM 2(C10 H9 N O2) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 K 2(K 1+) FORMUL 7 GOL 4(C3 H8 O3) FORMUL 13 HOH *250(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 GLY A 86 1 15 HELIX 6 AA6 HIS A 90 GLU A 95 5 6 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 ASP B 29 1 9 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 GLN B 84 1 13 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 PHE B 189 1 8 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 LEU B 323 1 17 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 VAL A 133 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 299 SHEET 6 AA1 8 ILE A 172 ALA A 176 1 N VAL A 175 O GLN A 263 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 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 301 SHEET 6 AA2 8 ILE B 172 ALA 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 C ACE C 1 N ARG C 2 1555 1555 1.33 LINK C HIS C 3 N ALY C 4 1555 1555 1.33 LINK C ALY C 4 N ALY C 5 1555 1555 1.33 LINK C ALY C 5 N MCM C 6 1555 1555 1.33 LINK C ACE D 1 N ARG D 2 1555 1555 1.33 LINK C HIS D 3 N ALY D 4 1555 1555 1.33 LINK C ALY D 4 N ALY D 5 1555 1555 1.33 LINK C ALY D 5 N MCM D 6 1555 1555 1.34 LINK OD2 ASP A 178 ZN ZN A 401 1555 1555 1.97 LINK ND1 HIS A 180 ZN ZN A 401 1555 1555 2.18 LINK O PHE A 189 K K A 402 1555 1555 2.60 LINK O THR A 192 K K A 402 1555 1555 2.85 LINK O VAL A 195 K K A 402 1555 1555 2.64 LINK O TYR A 225 K K A 402 1555 1555 2.89 LINK OD2 ASP A 267 ZN ZN A 401 1555 1555 2.08 LINK ZN ZN A 401 OH ALY C 5 1555 1555 2.31 LINK K K A 402 O HOH A 510 1555 1555 2.77 LINK K K A 402 O HOH A 561 1555 1555 2.81 LINK OD2 ASP B 178 ZN ZN B 401 1555 1555 1.97 LINK ND1 HIS B 180 ZN ZN B 401 1555 1555 2.14 LINK O PHE B 189 K K B 402 1555 1555 2.62 LINK O THR B 192 K K B 402 1555 1555 2.95 LINK O VAL B 195 K K B 402 1555 1555 2.66 LINK O TYR B 225 K K B 402 1555 1555 2.99 LINK OD2 ASP B 267 ZN ZN B 401 1555 1555 2.09 LINK ZN ZN B 401 OH ALY D 5 1555 1555 2.14 LINK K K B 402 O HOH B 521 1555 1555 2.73 LINK K K B 402 O HOH B 538 1555 1555 2.85 CISPEP 1 PHE A 208 PRO A 209 0 -1.98 CISPEP 2 GLY A 341 PRO A 342 0 -0.32 CISPEP 3 PHE B 208 PRO B 209 0 -1.09 CISPEP 4 GLY B 341 PRO B 342 0 0.93 SITE 1 AC1 2 ASP A 178 ASP A 267 SITE 1 AC2 6 PHE A 189 THR A 192 VAL A 195 TYR A 225 SITE 2 AC2 6 HOH A 510 HOH A 561 SITE 1 AC3 5 LYS A 145 GLU A 148 PRO A 209 HOH A 529 SITE 2 AC3 5 HOH A 536 SITE 1 AC4 2 ASP B 178 ASP B 267 SITE 1 AC5 6 PHE B 189 THR B 192 VAL B 195 TYR B 225 SITE 2 AC5 6 HOH B 521 HOH B 538 SITE 1 AC6 2 GLY B 271 HOH B 572 SITE 1 AC7 2 LYS B 52 MET B 54 SITE 1 AC8 3 LYS B 145 GLU B 148 HOH D 202 CRYST1 81.845 97.748 103.616 90.00 90.00 90.00 P 21 21 21 8 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 0.012218 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010230 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009651 0.00000