HEADER HYDROLASE 02-MAY-14 4QA2 TITLE CRYSTAL STRUCTURE OF I243N HDAC8 IN COMPLEX WITH SAHA 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 METALLOENZYME, HYDROLASE, HISTONE DEACETYLASE, ENZYME INHIBITOR KEYWDS 2 COMPLEX, CORNELIA DE LANGE SYNDROME, ARGINASE/DEACETYLASE FOLD EXPDTA X-RAY DIFFRACTION AUTHOR C.DECROOS,C.B.BOWMAN,J.-A.S.MOSER,K.E.CHRISTIANSON,M.A.DEARDORFF, AUTHOR 2 D.W.CHRISTIANSON REVDAT 3 20-SEP-23 4QA2 1 REMARK SEQADV LINK REVDAT 2 01-OCT-14 4QA2 1 JRNL REVDAT 1 06-AUG-14 4QA2 0 JRNL AUTH C.DECROOS,C.M.BOWMAN,J.A.MOSER,K.E.CHRISTIANSON, JRNL AUTH 2 M.A.DEARDORFF,D.W.CHRISTIANSON JRNL TITL COMPROMISED STRUCTURE AND FUNCTION OF HDAC8 MUTANTS JRNL TITL 2 IDENTIFIED IN CORNELIA DE LANGE SYNDROME SPECTRUM DISORDERS. JRNL REF ACS CHEM.BIOL. V. 9 2157 2014 JRNL REFN ISSN 1554-8929 JRNL PMID 25075551 JRNL DOI 10.1021/CB5003762 REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1370) 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) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 32999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.180 REMARK 3 FREE R VALUE TEST SET COUNT : 2369 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 46.6691 - 6.1073 1.00 1855 156 0.1532 0.1792 REMARK 3 2 6.1073 - 4.8492 1.00 1802 152 0.1618 0.1680 REMARK 3 3 4.8492 - 4.2367 1.00 1837 130 0.1339 0.1673 REMARK 3 4 4.2367 - 3.8495 1.00 1818 130 0.1430 0.1965 REMARK 3 5 3.8495 - 3.5737 1.00 1832 131 0.1645 0.2037 REMARK 3 6 3.5737 - 3.3631 1.00 1787 152 0.1841 0.2255 REMARK 3 7 3.3631 - 3.1947 1.00 1807 135 0.1899 0.2708 REMARK 3 8 3.1947 - 3.0556 1.00 1812 139 0.1930 0.2434 REMARK 3 9 3.0556 - 2.9380 1.00 1787 133 0.1957 0.2573 REMARK 3 10 2.9380 - 2.8366 1.00 1817 136 0.1927 0.2348 REMARK 3 11 2.8366 - 2.7480 1.00 1788 139 0.2091 0.2973 REMARK 3 12 2.7480 - 2.6694 1.00 1804 130 0.1936 0.3048 REMARK 3 13 2.6694 - 2.5992 1.00 1825 123 0.1961 0.2904 REMARK 3 14 2.5992 - 2.5357 1.00 1769 146 0.1932 0.2759 REMARK 3 15 2.5357 - 2.4781 1.00 1789 147 0.1879 0.2753 REMARK 3 16 2.4781 - 2.4254 0.99 1758 149 0.1874 0.2282 REMARK 3 17 2.4254 - 2.3769 0.96 1743 141 0.1953 0.2601 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.54 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 : 0.002 5796 REMARK 3 ANGLE : 0.657 7865 REMARK 3 CHIRALITY : 0.046 860 REMARK 3 PLANARITY : 0.003 1006 REMARK 3 DIHEDRAL : 11.704 2085 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 4QA2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : MIRRORS 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 : 33016 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.30800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.900 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: PDB ENTRY 3EWF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M (BIS(2-HYDROXYETHYL)-AMINO REMARK 280 -TRIS(HYDROXYMETHYL)-METHANE) (BISTRIS, PH = 6.5), 4 MM TRIS(2- REMARK 280 CARBOXYETHYL)PHOSPHINE (TCEP), 18% PEG 8000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 294K, PH 7.0 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 42.02850 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, 3 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 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 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 GLU A 95 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 LYS A 58 CG CD CE NZ REMARK 470 GLU A 85 CG CD OE1 OE2 REMARK 470 GLU A 106 CG CD OE1 OE2 REMARK 470 GLN A 363 CG CD OE1 NE2 REMARK 470 LYS B 36 CG CD CE NZ REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 GLN B 84 CG CD OE1 NE2 REMARK 470 ASP B 87 CG OD1 OD2 REMARK 470 ASP B 89 CG OD1 OD2 REMARK 470 GLU B 238 CG CD OE1 OE2 REMARK 470 GLN B 253 CG CD OE1 NE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 253 CG CD OE1 NE2 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 GLU A 85 -80.27 -108.46 REMARK 500 ASN A 256 71.75 51.91 REMARK 500 SER A 276 -79.86 -106.02 REMARK 500 HIS A 334 -166.96 -165.54 REMARK 500 ASP B 88 -151.60 -75.03 REMARK 500 TYR B 100 -74.62 -61.43 REMARK 500 SER B 276 -76.76 -103.96 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 K A 401 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 OD1 REMARK 620 2 ASP A 176 O 74.8 REMARK 620 3 ASP A 178 O 105.9 108.0 REMARK 620 4 HIS A 180 O 88.9 161.9 83.6 REMARK 620 5 SER A 199 OG 103.5 83.0 150.4 93.6 REMARK 620 6 LEU A 200 O 142.5 74.3 64.8 123.7 93.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 178 OD2 REMARK 620 2 HIS A 180 ND1 103.5 REMARK 620 3 ASP A 267 OD1 101.9 100.2 REMARK 620 4 SHH A 404 O2 155.2 98.6 85.1 REMARK 620 5 SHH A 404 O1 86.9 104.5 151.0 76.5 REMARK 620 N 1 2 3 4 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 73.2 REMARK 620 3 VAL A 195 O 110.8 87.3 REMARK 620 4 TYR A 225 O 159.9 123.7 82.8 REMARK 620 5 HOH A 501 O 93.0 94.9 155.6 75.8 REMARK 620 6 HOH A 526 O 69.8 142.1 113.3 91.4 79.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 401 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 176 OD1 REMARK 620 2 ASP B 176 O 72.9 REMARK 620 3 ASP B 178 O 104.3 106.6 REMARK 620 4 HIS B 180 O 92.1 163.2 84.0 REMARK 620 5 SER B 199 OG 105.4 84.0 150.3 93.1 REMARK 620 6 LEU B 200 O 139.1 73.4 64.6 123.3 93.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 178 OD1 REMARK 620 2 HIS B 180 ND1 104.5 REMARK 620 3 ASP B 267 OD2 100.9 100.7 REMARK 620 4 SHH B 404 O1 82.3 97.4 160.2 REMARK 620 5 SHH B 404 O2 150.7 100.1 89.8 79.0 REMARK 620 N 1 2 3 4 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 71.5 REMARK 620 3 VAL B 195 O 109.0 82.1 REMARK 620 4 TYR B 225 O 162.7 119.3 86.7 REMARK 620 5 HOH B 514 O 90.5 95.7 158.3 75.5 REMARK 620 6 HOH B 516 O 78.6 149.3 115.0 88.2 77.4 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 K 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 ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SHH A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K 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 ZN B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SHH B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QA0 RELATED DB: PDB REMARK 900 RELATED ID: 4QA1 RELATED DB: PDB REMARK 900 RELATED ID: 4QA2 RELATED DB: PDB REMARK 900 RELATED ID: 4QA3 RELATED DB: PDB REMARK 900 RELATED ID: 4QA4 RELATED DB: PDB REMARK 900 RELATED ID: 4QA5 RELATED DB: PDB REMARK 900 RELATED ID: 4QA6 RELATED DB: PDB REMARK 900 RELATED ID: 4QA7 RELATED DB: PDB DBREF 4QA2 A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 DBREF 4QA2 B 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 SEQADV 4QA2 ASN A 243 UNP Q9BY41 ILE 243 ENGINEERED MUTATION SEQADV 4QA2 ILE A 378 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 GLU A 379 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 GLY A 380 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 ARG A 381 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 GLY A 382 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 SER A 383 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 HIS A 384 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 HIS A 385 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 HIS A 386 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 HIS A 387 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 HIS A 388 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 HIS A 389 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 ASN B 243 UNP Q9BY41 ILE 243 ENGINEERED MUTATION SEQADV 4QA2 ILE B 378 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 GLU B 379 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 GLY B 380 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 ARG B 381 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 GLY B 382 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 SER B 383 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 HIS B 384 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 HIS B 385 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 HIS B 386 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 HIS B 387 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 HIS B 388 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA2 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 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 ASN 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 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 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 ASN 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 K A 401 1 HET K A 402 1 HET ZN A 403 1 HET SHH A 404 19 HET K B 401 1 HET K B 402 1 HET ZN B 403 1 HET SHH B 404 19 HET GOL B 405 6 HET GOL B 406 6 HETNAM K POTASSIUM ION HETNAM ZN ZINC ION HETNAM SHH OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE HETNAM GOL GLYCEROL HETSYN SHH SAHA HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 K 4(K 1+) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 SHH 2(C14 H20 N2 O3) FORMUL 11 GOL 2(C3 H8 O3) FORMUL 13 HOH *180(H2 O) HELIX 1 1 SER A 21 SER A 30 1 10 HELIX 2 2 LYS A 36 TYR A 48 1 13 HELIX 3 3 ALA A 49 MET A 54 5 6 HELIX 4 4 SER A 63 ALA A 68 1 6 HELIX 5 5 THR A 72 GLU A 85 1 14 HELIX 6 6 GLY A 107 ASP A 128 1 22 HELIX 7 7 ASN A 156 ARG A 166 1 11 HELIX 8 8 GLY A 182 PHE A 189 1 8 HELIX 9 9 LEU A 219 ARG A 223 5 5 HELIX 10 10 GLN A 236 ASN A 256 1 21 HELIX 11 11 THR A 280 GLN A 293 1 14 HELIX 12 12 ASN A 307 LEU A 323 1 17 HELIX 13 13 PHE A 336 GLY A 341 5 6 HELIX 14 14 GLU A 358 LEU A 373 1 16 HELIX 15 15 SER B 21 ASP B 29 1 9 HELIX 16 16 LYS B 36 TYR B 48 1 13 HELIX 17 17 ALA B 49 MET B 54 5 6 HELIX 18 18 SER B 63 ALA B 68 1 6 HELIX 19 19 THR B 72 SER B 83 1 12 HELIX 20 20 GLY B 107 ASP B 128 1 22 HELIX 21 21 ASN B 156 ARG B 166 1 11 HELIX 22 22 GLY B 182 SER B 190 1 9 HELIX 23 23 LEU B 219 ARG B 223 5 5 HELIX 24 24 GLN B 236 ASN B 256 1 21 HELIX 25 25 THR B 280 GLN B 293 1 14 HELIX 26 26 ASN B 307 GLY B 324 1 18 HELIX 27 27 PHE B 336 GLY B 341 5 6 HELIX 28 28 GLU B 358 LEU B 373 1 16 SHEET 1 A 8 ARG A 55 VAL A 57 0 SHEET 2 A 8 VAL A 17 ILE A 19 1 N TYR A 18 O ARG A 55 SHEET 3 A 8 VAL A 133 ASN A 136 1 O VAL A 133 N VAL A 17 SHEET 4 A 8 ALA A 297 LEU A 301 1 O ILE A 300 N ALA A 134 SHEET 5 A 8 ALA A 259 GLN A 263 1 N VAL A 260 O ALA A 297 SHEET 6 A 8 ILE A 172 ASP A 176 1 N VAL A 175 O GLN A 263 SHEET 7 A 8 VAL A 195 LYS A 202 1 O VAL A 198 N TYR A 174 SHEET 8 A 8 SER A 226 ILE A 231 1 O VAL A 227 N THR A 197 SHEET 1 B 8 ARG B 55 VAL B 57 0 SHEET 2 B 8 VAL B 17 ILE B 19 1 N TYR B 18 O ARG B 55 SHEET 3 B 8 VAL B 133 ASN B 136 1 O ILE B 135 N VAL B 17 SHEET 4 B 8 ALA B 297 LEU B 301 1 O ILE B 300 N ALA B 134 SHEET 5 B 8 ALA B 259 GLN B 263 1 N VAL B 260 O ALA B 297 SHEET 6 B 8 ILE B 172 ASP B 176 1 N VAL B 175 O GLN B 263 SHEET 7 B 8 VAL B 195 LYS B 202 1 O VAL B 198 N TYR B 174 SHEET 8 B 8 SER B 226 ILE B 231 1 O VAL B 227 N THR B 197 LINK OD1 ASP A 176 K K A 401 1555 1555 2.77 LINK O ASP A 176 K K A 401 1555 1555 2.82 LINK O ASP A 178 K K A 401 1555 1555 2.70 LINK OD2 ASP A 178 ZN ZN A 403 1555 1555 2.00 LINK O HIS A 180 K K A 401 1555 1555 2.81 LINK ND1 HIS A 180 ZN ZN A 403 1555 1555 2.07 LINK O PHE A 189 K K A 402 1555 1555 2.65 LINK O THR A 192 K K A 402 1555 1555 2.97 LINK O VAL A 195 K K A 402 1555 1555 2.69 LINK OG SER A 199 K K A 401 1555 1555 3.00 LINK O LEU A 200 K K A 401 1555 1555 2.72 LINK O TYR A 225 K K A 402 1555 1555 2.98 LINK OD1 ASP A 267 ZN ZN A 403 1555 1555 2.07 LINK K K A 402 O HOH A 501 1555 1555 2.74 LINK K K A 402 O HOH A 526 1555 1555 2.91 LINK ZN ZN A 403 O2 SHH A 404 1555 1555 2.15 LINK ZN ZN A 403 O1 SHH A 404 1555 1555 2.19 LINK OD1 ASP B 176 K K B 401 1555 1555 2.82 LINK O ASP B 176 K K B 401 1555 1555 2.89 LINK O ASP B 178 K K B 401 1555 1555 2.72 LINK OD1 ASP B 178 ZN ZN B 403 1555 1555 2.01 LINK O HIS B 180 K K B 401 1555 1555 2.76 LINK ND1 HIS B 180 ZN ZN B 403 1555 1555 2.22 LINK O PHE B 189 K K B 402 1555 1555 2.64 LINK O THR B 192 K K B 402 1555 1555 2.91 LINK O VAL B 195 K K B 402 1555 1555 2.72 LINK OG SER B 199 K K B 401 1555 1555 3.13 LINK O LEU B 200 K K B 401 1555 1555 2.71 LINK O TYR B 225 K K B 402 1555 1555 2.90 LINK OD2 ASP B 267 ZN ZN B 403 1555 1555 2.03 LINK K K B 402 O HOH B 514 1555 1555 2.82 LINK K K B 402 O HOH B 516 1555 1555 2.80 LINK ZN ZN B 403 O1 SHH B 404 1555 1555 2.08 LINK ZN ZN B 403 O2 SHH B 404 1555 1555 2.17 CISPEP 1 PHE A 208 PRO A 209 0 -3.04 CISPEP 2 GLY A 341 PRO A 342 0 -1.25 CISPEP 3 PHE B 208 PRO B 209 0 -1.51 CISPEP 4 GLY B 341 PRO B 342 0 1.37 CISPEP 5 VAL B 377 ILE B 378 0 -5.67 SITE 1 AC1 5 ASP A 176 ASP A 178 HIS A 180 SER A 199 SITE 2 AC1 5 LEU A 200 SITE 1 AC2 6 PHE A 189 THR A 192 VAL A 195 TYR A 225 SITE 2 AC2 6 HOH A 501 HOH A 526 SITE 1 AC3 4 ASP A 178 HIS A 180 ASP A 267 SHH A 404 SITE 1 AC4 14 TYR A 100 HIS A 142 HIS A 143 GLY A 151 SITE 2 AC4 14 PHE A 152 ASP A 178 HIS A 180 PHE A 208 SITE 3 AC4 14 ASP A 267 GLY A 304 TYR A 306 ZN A 403 SITE 4 AC4 14 PRO B 273 SHH B 404 SITE 1 AC5 5 ASP B 176 ASP B 178 HIS B 180 SER B 199 SITE 2 AC5 5 LEU B 200 SITE 1 AC6 6 PHE B 189 THR B 192 VAL B 195 TYR B 225 SITE 2 AC6 6 HOH B 514 HOH B 516 SITE 1 AC7 4 ASP B 178 HIS B 180 ASP B 267 SHH B 404 SITE 1 AC8 15 PRO A 273 SHH A 404 TYR B 100 HIS B 142 SITE 2 AC8 15 HIS B 143 GLY B 151 PHE B 152 ASP B 178 SITE 3 AC8 15 HIS B 180 PHE B 208 ASP B 267 GLY B 304 SITE 4 AC8 15 TYR B 306 ZN B 403 HOH B 521 SITE 1 AC9 6 GLY B 271 ASN B 310 ILE B 348 THR B 349 SITE 2 AC9 6 SER B 351 HOH B 531 SITE 1 BC1 2 ALA B 188 PHE B 189 CRYST1 53.017 84.057 94.381 90.00 98.60 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 0.018862 0.000000 0.002852 0.00000 SCALE2 0.000000 0.011897 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010716 0.00000