HEADER HYDROLASE 14-OCT-08 3EW8 TITLE CRYSTAL STRUCTURE ANALYSIS OF HUMAN HDAC8 D101L VARIANT 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: CDA07, HDAC8, HDACL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHD2-XA-HIS KEYWDS HYDROLASE, HDAC, METALLOENZYME, ARGINASE FOLD, HDAC8, HISTONE KEYWDS 2 DEACETYLASE, HYDROXAMATE INHIBITOR, UNLIGANDED, CHROMATIN REGULATOR, KEYWDS 3 NUCLEUS, REPRESSOR, TRANSCRIPTION, TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR D.P.DOWLING,S.L.GANTT,S.G.GATTIS,C.A.FIERKE,D.W.CHRISTIANSON REVDAT 5 06-SEP-23 3EW8 1 REMARK REVDAT 4 20-OCT-21 3EW8 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3EW8 1 VERSN REVDAT 2 02-MAR-11 3EW8 1 HETNAM HETSYN REVDAT 1 30-DEC-08 3EW8 0 JRNL AUTH D.P.DOWLING,S.L.GANTT,S.G.GATTIS,C.A.FIERKE,D.W.CHRISTIANSON JRNL TITL STRUCTURAL STUDIES OF HUMAN HISTONE DEACETYLASE 8 AND ITS JRNL TITL 2 SITE-SPECIFIC VARIANTS COMPLEXED WITH SUBSTRATE AND JRNL TITL 3 INHIBITORS. JRNL REF BIOCHEMISTRY V. 47 13554 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 19053282 JRNL DOI 10.1021/BI801610C REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 267623.750 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 38536 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2319 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5462 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 374 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2784 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 253 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.96000 REMARK 3 B22 (A**2) : 6.68000 REMARK 3 B33 (A**2) : -5.72000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.010 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.170 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.760 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.130 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.110 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 58.54 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : B3N.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : PROSTHETICS.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : B3N.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : PROSTHETICS.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3EW8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049844. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97926 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39760 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.53500 REMARK 200 FOR SHELL : 3.900 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: 1T67 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROP COMPOSITION: 25 MM TRIS, 2.5% REMARK 280 GLYCEROL, 75 MM KCL, 1-5% PEG MME 550, 50 MM MES, 1 MM TRI(2- REMARK 280 CARBOXYETHYL)PHOSPHINE (TCEP), 0.03 MM GLY-GLY-GLY, PH 5.8, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 45.27850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.45550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.27850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.45550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 664 LIES ON A SPECIAL POSITION. 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 379 REMARK 465 GLY A 380 REMARK 465 ARG A 381 REMARK 465 SER A 382 REMARK 465 HIS 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 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 GLU A 85 OE1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN A 307 N - CA - C ANGL. DEV. = -18.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 70 -54.06 -125.40 REMARK 500 PHE A 152 -0.90 72.98 REMARK 500 TYR A 224 -0.25 84.67 REMARK 500 CYS A 275 52.63 35.86 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 600 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 O REMARK 620 2 ASP A 176 OD1 71.1 REMARK 620 3 ASP A 178 O 107.1 102.2 REMARK 620 4 HIS A 180 O 158.6 88.5 83.1 REMARK 620 5 SER A 199 OG 85.0 103.0 154.4 93.5 REMARK 620 6 LEU A 200 O 79.5 145.9 70.0 121.9 90.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 178 OD2 REMARK 620 2 HIS A 180 ND1 102.4 REMARK 620 3 ASP A 267 OD2 108.2 101.7 REMARK 620 4 B3N A 501 O2 148.2 102.6 85.5 REMARK 620 5 B3N A 501 O4 93.4 97.1 147.3 64.2 REMARK 620 6 HOH A 603 O 147.7 101.6 87.6 2.1 62.4 REMARK 620 7 HOH A 604 O 89.8 98.1 149.5 67.5 3.6 65.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 602 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 189 O REMARK 620 2 THR A 192 O 78.4 REMARK 620 3 VAL A 195 O 117.5 86.3 REMARK 620 4 TYR A 225 O 155.3 119.0 83.0 REMARK 620 5 HOH A 605 O 71.4 149.2 112.5 88.4 REMARK 620 6 HOH A 609 O 88.3 94.9 153.7 73.5 78.8 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 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B3N A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 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: 2V5W RELATED DB: PDB REMARK 900 Y306F VARIANT OF HDAC8 COMPLEXED WITH IDENTICAL SUBSTRATE MOLECULE REMARK 900 RELATED ID: 3EWF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF HUMAN HDAC8 H143A VARIANT COMPLEXED REMARK 900 WITH SUBSTRATE DBREF 3EW8 A 1 377 UNP Q9BY41 HDAC8_HUMAN 1 377 SEQADV 3EW8 LEU A 101 UNP Q9BY41 ASP 101 ENGINEERED MUTATION SEQADV 3EW8 ILE A 378 UNP Q9BY41 EXPRESSION TAG SEQADV 3EW8 GLU A 379 UNP Q9BY41 EXPRESSION TAG SEQADV 3EW8 GLY A 380 UNP Q9BY41 EXPRESSION TAG SEQADV 3EW8 ARG A 381 UNP Q9BY41 EXPRESSION TAG SEQADV 3EW8 SER A 382 UNP Q9BY41 EXPRESSION TAG SEQADV 3EW8 HIS A 383 UNP Q9BY41 EXPRESSION TAG SEQADV 3EW8 HIS A 384 UNP Q9BY41 EXPRESSION TAG SEQADV 3EW8 HIS A 385 UNP Q9BY41 EXPRESSION TAG SEQADV 3EW8 HIS A 386 UNP Q9BY41 EXPRESSION TAG SEQADV 3EW8 HIS A 387 UNP Q9BY41 EXPRESSION TAG SEQADV 3EW8 HIS A 388 UNP Q9BY41 EXPRESSION TAG SEQRES 1 A 388 MET GLU GLU PRO GLU GLU PRO ALA ASP SER GLY GLN SER SEQRES 2 A 388 LEU VAL PRO VAL TYR ILE TYR SER PRO GLU TYR VAL SER SEQRES 3 A 388 MET CYS ASP SER LEU ALA LYS ILE PRO LYS ARG ALA SER SEQRES 4 A 388 MET VAL HIS SER LEU ILE GLU ALA TYR ALA LEU HIS LYS SEQRES 5 A 388 GLN MET ARG ILE VAL LYS PRO LYS VAL ALA SER MET GLU SEQRES 6 A 388 GLU MET ALA THR PHE HIS THR ASP ALA TYR LEU GLN HIS SEQRES 7 A 388 LEU GLN LYS VAL SER GLN GLU GLY ASP ASP ASP HIS PRO SEQRES 8 A 388 ASP SER ILE GLU TYR GLY LEU GLY TYR LEU CYS PRO ALA SEQRES 9 A 388 THR GLU GLY ILE PHE ASP TYR ALA ALA ALA ILE GLY GLY SEQRES 10 A 388 ALA THR ILE THR ALA ALA GLN CYS LEU ILE ASP GLY MET SEQRES 11 A 388 CYS LYS VAL ALA ILE ASN TRP SER GLY GLY TRP HIS HIS SEQRES 12 A 388 ALA LYS LYS ASP GLU ALA SER GLY PHE CYS TYR LEU ASN SEQRES 13 A 388 ASP ALA VAL LEU GLY ILE LEU ARG LEU ARG ARG LYS PHE SEQRES 14 A 388 GLU ARG ILE LEU TYR VAL ASP LEU ASP LEU HIS HIS GLY SEQRES 15 A 388 ASP GLY VAL GLU ASP ALA PHE SER PHE THR SER LYS VAL SEQRES 16 A 388 MET THR VAL SER LEU HIS LYS PHE SER PRO GLY PHE PHE SEQRES 17 A 388 PRO GLY THR GLY ASP VAL SER ASP VAL GLY LEU GLY LYS SEQRES 18 A 388 GLY ARG TYR TYR SER VAL ASN VAL PRO ILE GLN ASP GLY SEQRES 19 A 388 ILE GLN ASP GLU LYS TYR TYR GLN ILE CYS GLU SER VAL SEQRES 20 A 388 LEU LYS GLU VAL TYR GLN ALA PHE ASN PRO LYS ALA VAL SEQRES 21 A 388 VAL LEU GLN LEU GLY ALA ASP THR ILE ALA GLY ASP PRO SEQRES 22 A 388 MET CYS SER PHE ASN MET THR PRO VAL GLY ILE GLY LYS SEQRES 23 A 388 CYS LEU LYS TYR ILE LEU GLN TRP GLN LEU ALA THR LEU SEQRES 24 A 388 ILE LEU GLY GLY GLY GLY TYR ASN LEU ALA ASN THR ALA SEQRES 25 A 388 ARG CYS TRP THR TYR LEU THR GLY VAL ILE LEU GLY LYS SEQRES 26 A 388 THR LEU SER SER GLU ILE PRO ASP HIS GLU PHE PHE THR SEQRES 27 A 388 ALA TYR GLY PRO ASP TYR VAL LEU GLU ILE THR PRO SER SEQRES 28 A 388 CYS ARG PRO ASP ARG ASN GLU PRO HIS ARG ILE GLN GLN SEQRES 29 A 388 ILE LEU ASN TYR ILE LYS GLY ASN LEU LYS HIS VAL VAL SEQRES 30 A 388 ILE GLU GLY ARG SER HIS HIS HIS HIS HIS HIS HET K A 600 1 HET ZN A 601 1 HET K A 602 1 HET B3N A 501 22 HET BME A 502 4 HET GOL A 505 6 HET GOL A 506 6 HET GOL A 507 6 HETNAM K POTASSIUM ION HETNAM ZN ZINC ION HETNAM B3N 4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7- HETNAM 2 B3N OXOHEPTYL]BENZAMIDE HETNAM BME BETA-MERCAPTOETHANOL HETNAM GOL GLYCEROL HETSYN B3N M344 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 K 2(K 1+) FORMUL 3 ZN ZN 2+ FORMUL 5 B3N C16 H25 N3 O3 FORMUL 6 BME C2 H6 O S FORMUL 7 GOL 3(C3 H8 O3) FORMUL 10 HOH *253(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 GLY A 86 1 15 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 GLY A 324 1 18 HELIX 13 13 PHE A 336 GLY A 341 5 6 HELIX 14 14 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 VAL A 57 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 301 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 229 N SER A 199 LINK O ASP A 176 K K A 600 1555 1555 2.75 LINK OD1 ASP A 176 K K A 600 1555 1555 2.75 LINK O ASP A 178 K K A 600 1555 1555 2.66 LINK OD2 ASP A 178 ZN ZN A 601 1555 1555 2.00 LINK O HIS A 180 K K A 600 1555 1555 2.74 LINK ND1 HIS A 180 ZN ZN A 601 1555 1555 2.13 LINK O PHE A 189 K K A 602 1555 1555 2.59 LINK O THR A 192 K K A 602 1555 1555 2.82 LINK O VAL A 195 K K A 602 1555 1555 2.59 LINK OG SER A 199 K K A 600 1555 1555 2.91 LINK O LEU A 200 K K A 600 1555 1555 2.63 LINK O TYR A 225 K K A 602 1555 1555 3.01 LINK OD2 ASP A 267 ZN ZN A 601 1555 1555 1.98 LINK O2 AB3N A 501 ZN ZN A 601 1555 1555 2.29 LINK O4 AB3N A 501 ZN ZN A 601 1555 1555 2.53 LINK ZN ZN A 601 O BHOH A 603 1555 1555 2.13 LINK ZN ZN A 601 O BHOH A 604 1555 1555 2.33 LINK K K A 602 O HOH A 605 1555 1555 2.79 LINK K K A 602 O HOH A 609 1555 1555 2.79 CISPEP 1 PHE A 208 PRO A 209 0 -0.11 CISPEP 2 GLY A 341 PRO A 342 0 0.18 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 ASP A 178 HIS A 180 ASP A 267 B3N A 501 SITE 2 AC2 6 HOH A 603 HOH A 604 SITE 1 AC3 6 PHE A 189 THR A 192 VAL A 195 TYR A 225 SITE 2 AC3 6 HOH A 605 HOH A 609 SITE 1 AC4 19 TYR A 100 LEU A 101 HIS A 142 HIS A 143 SITE 2 AC4 19 PHE A 152 ASP A 178 HIS A 180 PHE A 208 SITE 3 AC4 19 ASP A 267 MET A 274 GLY A 304 TYR A 306 SITE 4 AC4 19 GOL A 505 GOL A 506 GOL A 507 ZN A 601 SITE 5 AC4 19 HOH A 603 HOH A 604 HOH A 664 SITE 1 AC5 3 ARG A 167 GLN A 236 ASP A 355 SITE 1 AC6 7 HIS A 143 GLY A 151 GLY A 303 GLY A 304 SITE 2 AC6 7 TYR A 306 B3N A 501 HOH A 604 SITE 1 AC7 8 TRP A 141 HIS A 143 GLY A 151 GLY A 303 SITE 2 AC7 8 GLY A 304 TYR A 306 B3N A 501 HOH A 604 SITE 1 AC8 8 TRP A 141 HIS A 143 GLY A 151 GLY A 303 SITE 2 AC8 8 GLY A 304 TYR A 306 B3N A 501 HOH A 604 CRYST1 90.557 88.911 52.378 90.00 90.00 90.00 P 21 21 2 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 0.011043 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011247 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019092 0.00000