HEADER HYDROLASE 02-MAY-14 4QA4 TITLE CRYSTAL STRUCTURE OF H334R HDAC8 IN COMPLEX WITH M344 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 8; COMPND 3 CHAIN: A; 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 4QA4 1 REMARK SEQADV LINK REVDAT 2 01-OCT-14 4QA4 1 JRNL REVDAT 1 06-AUG-14 4QA4 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. 1.98 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 28629 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2062 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 42.5804 - 4.8809 1.00 1903 152 0.1585 0.1700 REMARK 3 2 4.8809 - 3.8749 1.00 1796 152 0.1515 0.1512 REMARK 3 3 3.8749 - 3.3853 1.00 1803 136 0.1709 0.2193 REMARK 3 4 3.3853 - 3.0759 1.00 1784 140 0.1876 0.2069 REMARK 3 5 3.0759 - 2.8555 1.00 1785 120 0.1917 0.2404 REMARK 3 6 2.8555 - 2.6872 1.00 1749 155 0.1980 0.2326 REMARK 3 7 2.6872 - 2.5526 1.00 1781 138 0.1849 0.2397 REMARK 3 8 2.5526 - 2.4415 1.00 1724 130 0.1895 0.2163 REMARK 3 9 2.4415 - 2.3475 1.00 1800 135 0.1860 0.2549 REMARK 3 10 2.3475 - 2.2665 1.00 1771 122 0.1908 0.2713 REMARK 3 11 2.2665 - 2.1957 1.00 1768 118 0.2063 0.2357 REMARK 3 12 2.1957 - 2.1329 1.00 1754 120 0.1973 0.2564 REMARK 3 13 2.1329 - 2.0767 1.00 1760 126 0.2290 0.2877 REMARK 3 14 2.0767 - 2.0261 1.00 1722 157 0.2456 0.3315 REMARK 3 15 2.0261 - 1.9800 0.97 1667 161 0.2742 0.3035 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.26 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 3008 REMARK 3 ANGLE : 0.769 4090 REMARK 3 CHIRALITY : 0.055 445 REMARK 3 PLANARITY : 0.003 519 REMARK 3 DIHEDRAL : 13.662 1091 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 4QA4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085795. 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 : 7.3 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 : 28649 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 11.00 REMARK 200 R MERGE FOR SHELL (I) : 1.19800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 3EWF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE (PH = 7.0), 4 MM REMARK 280 TRIS(2-CARBOXYETHYL)PHOSPHINE (TCEP), 20% PEG 8000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 294K, PH 7.3 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 35.79433 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 71.58867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 71.58867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.79433 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.0 KCAL/MOL 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 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -71.58867 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 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 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 ASP A 88 CG OD1 OD2 REMARK 470 ASP A 89 CG OD1 OD2 REMARK 470 GLU A 170 CG CD OE1 OE2 REMARK 470 GLU A 238 CG CD OE1 OE2 REMARK 470 GLU A 358 CG CD OE1 OE2 REMARK 470 LYS A 370 CG CD CE NZ 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 PHE A 70 -55.02 -127.45 REMARK 500 ASP A 89 30.02 -141.40 REMARK 500 SER A 276 -73.34 -117.58 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 503 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 OD1 REMARK 620 2 ASP A 176 O 73.1 REMARK 620 3 ASP A 178 O 103.7 105.6 REMARK 620 4 HIS A 180 O 88.9 161.3 83.1 REMARK 620 5 SER A 199 OG 104.7 85.6 151.5 94.5 REMARK 620 6 LEU A 200 O 145.0 77.8 66.0 120.8 91.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 178 OD2 REMARK 620 2 HIS A 180 ND1 102.8 REMARK 620 3 ASP A 267 OD2 108.3 104.5 REMARK 620 4 B3N A 501 O4 82.7 97.5 152.1 REMARK 620 5 B3N A 501 O2 158.5 87.1 87.1 77.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 504 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 189 O REMARK 620 2 THR A 192 O 75.4 REMARK 620 3 VAL A 195 O 114.5 85.5 REMARK 620 4 TYR A 225 O 159.5 118.6 82.9 REMARK 620 5 HOH A 604 O 90.4 92.7 153.6 74.9 REMARK 620 6 HOH A 608 O 73.2 147.7 114.4 90.1 80.1 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 B3N A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 507 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: 4QA5 RELATED DB: PDB REMARK 900 RELATED ID: 4QA6 RELATED DB: PDB REMARK 900 RELATED ID: 4QA7 RELATED DB: PDB DBREF 4QA4 A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 SEQADV 4QA4 ARG A 334 UNP Q9BY41 HIS 334 ENGINEERED MUTATION SEQADV 4QA4 ILE A 378 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA4 GLU A 379 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA4 GLY A 380 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA4 ARG A 381 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA4 GLY A 382 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA4 SER A 383 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA4 HIS A 384 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA4 HIS A 385 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA4 HIS A 386 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA4 HIS A 387 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA4 HIS A 388 UNP Q9BY41 EXPRESSION TAG SEQADV 4QA4 HIS A 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 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 ARG 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 HET B3N A 501 22 HET ZN A 502 1 HET K A 503 1 HET K A 504 1 HET GOL A 505 6 HET GOL A 506 12 HET GOL A 507 6 HETNAM B3N 4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7- HETNAM 2 B3N OXOHEPTYL]BENZAMIDE HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETSYN B3N M344 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 B3N C16 H25 N3 O3 FORMUL 3 ZN ZN 2+ FORMUL 4 K 2(K 1+) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 9 HOH *137(H2 O) HELIX 1 1 SER A 21 ASP A 29 1 9 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 GLN A 84 1 13 HELIX 6 6 HIS A 90 GLY A 97 5 8 HELIX 7 7 GLY A 107 ASP A 128 1 22 HELIX 8 8 ASN A 156 ARG A 166 1 11 HELIX 9 9 GLY A 182 PHE A 189 1 8 HELIX 10 10 LEU A 219 ARG A 223 5 5 HELIX 11 11 GLN A 236 ASN A 256 1 21 HELIX 12 12 THR A 280 GLN A 293 1 14 HELIX 13 13 ASN A 307 GLY A 324 1 18 HELIX 14 14 PHE A 336 GLY A 341 5 6 HELIX 15 15 GLU A 358 LYS A 374 1 17 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 LEU A 262 O LEU A 299 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 MET A 196 N TYR A 174 SHEET 8 A 8 SER A 226 ILE A 231 1 O VAL A 227 N THR A 197 LINK OD1 ASP A 176 K K A 503 1555 1555 2.70 LINK O ASP A 176 K K A 503 1555 1555 2.81 LINK OD2 ASP A 178 ZN ZN A 502 1555 1555 1.97 LINK O ASP A 178 K K A 503 1555 1555 2.73 LINK ND1 HIS A 180 ZN ZN A 502 1555 1555 2.10 LINK O HIS A 180 K K A 503 1555 1555 2.74 LINK O PHE A 189 K K A 504 1555 1555 2.69 LINK O THR A 192 K K A 504 1555 1555 2.91 LINK O VAL A 195 K K A 504 1555 1555 2.63 LINK OG SER A 199 K K A 503 1555 1555 2.90 LINK O LEU A 200 K K A 503 1555 1555 2.68 LINK O TYR A 225 K K A 504 1555 1555 3.06 LINK OD2 ASP A 267 ZN ZN A 502 1555 1555 2.00 LINK O4 B3N A 501 ZN ZN A 502 1555 1555 2.04 LINK O2 B3N A 501 ZN ZN A 502 1555 1555 2.32 LINK K K A 504 O HOH A 604 1555 1555 2.74 LINK K K A 504 O HOH A 608 1555 1555 2.75 CISPEP 1 PHE A 208 PRO A 209 0 -2.34 CISPEP 2 GLY A 341 PRO A 342 0 3.60 SITE 1 AC1 14 TYR A 100 ASP A 101 HIS A 142 HIS A 143 SITE 2 AC1 14 GLY A 151 PHE A 152 ASP A 178 HIS A 180 SITE 3 AC1 14 ASP A 267 PRO A 273 MET A 274 TYR A 306 SITE 4 AC1 14 ZN A 502 HOH A 702 SITE 1 AC2 4 ASP A 178 HIS A 180 ASP A 267 B3N A 501 SITE 1 AC3 5 ASP A 176 ASP A 178 HIS A 180 SER A 199 SITE 2 AC3 5 LEU A 200 SITE 1 AC4 6 PHE A 189 THR A 192 VAL A 195 TYR A 225 SITE 2 AC4 6 HOH A 604 HOH A 608 SITE 1 AC5 4 GLN A 236 SER A 351 CYS A 352 ARG A 353 SITE 1 AC6 7 LYS A 289 TYR A 317 VAL A 321 GLY A 324 SITE 2 AC6 7 LYS A 325 THR A 326 HOH A 617 SITE 1 AC7 5 SER A 215 ASP A 216 VAL A 217 GLY A 218 SITE 2 AC7 5 ARG A 223 CRYST1 80.665 80.665 107.383 90.00 90.00 120.00 P 31 2 1 6 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 0.012397 0.007157 0.000000 0.00000 SCALE2 0.000000 0.014315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009312 0.00000