HEADER HYDROLASE 14-JUN-16 5KH9 TITLE CRYSTAL STRUCTURE OF A LOW OCCUPANCY FRAGMENT CANDIDATE (5-[(4- TITLE 2 ISOPROPYLPHENYL)AMINO]-6-METHYL-1,2,4-TRIAZIN-3(2H)-ONE) BOUND IN THE TITLE 3 UBIQUITIN BINDING POCKET OF THE HDAC6 ZINC-FINGER DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HD6; COMPND 5 EC: 3.5.1.98; COMPND 6 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: HDAC6, KIAA0901, JM21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-LIC KEYWDS HISTONE DEACETYLASE, HDAC, HDAC6, FRAGMENT SCREENING, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, SGC, DIAMOND I04-1 XCHEM, PANDDA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.J.HARDING,W.TEMPEL,M.RAVICHANDRAN,P.COLLINS,N.PEARCE,J.BRANDAO- AUTHOR 2 NETO,A.DOUANGAMATH,M.SCHAPIRA,C.BOUNTRA,A.M.EDWARDS,F.VON DELFT, AUTHOR 3 V.SANTHAKUMAR,C.M.ARROWSMITH,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 27-SEP-23 5KH9 1 REMARK REVDAT 3 27-FEB-19 5KH9 1 JRNL REVDAT 2 21-MAR-18 5KH9 1 JRNL REMARK REVDAT 1 27-JUL-16 5KH9 0 JRNL AUTH R.J.HARDING,R.FERREIRA DE FREITAS,P.COLLINS,I.FRANZONI, JRNL AUTH 2 M.RAVICHANDRAN,H.OUYANG,K.A.JUAREZ-ORNELAS,M.LAUTENS, JRNL AUTH 3 M.SCHAPIRA,F.VON DELFT,V.SANTHAKUMAR,C.H.ARROWSMITH JRNL TITL SMALL MOLECULE ANTAGONISTS OF THE INTERACTION BETWEEN THE JRNL TITL 2 HISTONE DEACETYLASE 6 ZINC-FINGER DOMAIN AND UBIQUITIN. JRNL REF J. MED. CHEM. V. 60 9090 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 29019676 JRNL DOI 10.1021/ACS.JMEDCHEM.7B00933 REMARK 2 REMARK 2 RESOLUTION. 1.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0151 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 44074 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 + TEST SET) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2104 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3111 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 158 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 778 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.75000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : 1.15000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.025 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.024 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.020 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.931 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 897 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 797 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1241 ; 1.615 ; 1.921 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1839 ; 1.111 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 114 ; 6.316 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 42 ;32.088 ;24.762 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 122 ;11.439 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 1 ; 8.940 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 129 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1139 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 228 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 430 ; 1.432 ; 1.248 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 431 ; 1.430 ; 1.248 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 543 ; 1.978 ; 1.881 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1694 ; 2.231 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 31 ;33.838 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1739 ;16.791 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USERS OF THIS CRYSTAL STRUCTURE: VERIFY REMARK 3 OUR INTEPRETION OF THE ELECTRON DENSITY. AMPLITUDES AND UNMERGED REMARK 3 INTENSITIES ARE INCLUDED WITH THIS DEPOSITION. DIFFRACTION REMARK 3 IMAGES WILL BE DEPOSITED IN A PUBLIC REPOSITORY. GEOMETRY REMARK 3 RESTRAINTS FOR THE FRAGMENT CANDIDATE WERE PREPARED WITH GRADE. REMARK 3 AMBIGUOUS DIFFERENCE DENSITY SUGGESTS SOME FORM OF COVALENT REMARK 3 MODIFICATION OF CYS1147. REMARK 4 REMARK 4 5KH9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222213. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.26 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46238 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.070 REMARK 200 RESOLUTION RANGE LOW (A) : 34.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.95700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDBID 3C5K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M NA-FORMATE, 0.2M NA-ACETATE PH4.6, REMARK 280 5% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K 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 20.71700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.27450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.07850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.27450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.71700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.07850 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 TOTAL BURIED SURFACE AREA: 320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 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 GLY A 1107 REMARK 465 SER A 1108 REMARK 465 GLU A 1209 REMARK 465 ASP A 1210 REMARK 465 MET A 1211 REMARK 465 PRO A 1212 REMARK 465 HIS A 1213 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 ILE A1177 CD1 REMARK 470 GLN A1204 CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 1148 UNK UNX A 1306 1.56 REMARK 500 SG CYS A 1148 UNK UNX A 1307 1.56 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A1141 OE1 - CD - OE2 ANGL. DEV. = -8.5 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 ASP A1135 -61.08 -93.84 REMARK 500 ASP A1135 -61.10 -93.80 REMARK 500 ILE A1157 -103.62 -101.13 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 A1303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1113 SG REMARK 620 2 HIS A1115 ND1 110.2 REMARK 620 3 CYS A1183 SG 117.5 99.0 REMARK 620 4 CYS A1186 SG 111.4 106.5 111.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1133 SG REMARK 620 2 CYS A1136 SG 109.8 REMARK 620 3 CYS A1153 SG 113.5 115.1 REMARK 620 4 HIS A1160 ND1 107.3 110.3 100.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1145 SG REMARK 620 2 HIS A1164 NE2 116.0 REMARK 620 3 HIS A1170 ND1 109.8 111.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1339 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A1156 O REMARK 620 2 ILE A1157 O 81.4 REMARK 620 3 HOH A1458 O 88.7 89.6 REMARK 620 N 1 2 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 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 1304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6T5 A 1305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 1339 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KH3 RELATED DB: PDB REMARK 900 RELATED ID: 5KH7 RELATED DB: PDB REMARK 900 RELATED ID: 5B8D RELATED DB: PDB DBREF 5KH9 A 1109 1213 UNP Q9UBN7 HDAC6_HUMAN 1109 1213 SEQADV 5KH9 GLY A 1107 UNP Q9UBN7 EXPRESSION TAG SEQADV 5KH9 SER A 1108 UNP Q9UBN7 EXPRESSION TAG SEQRES 1 A 107 GLY SER PRO LEU PRO TRP CYS PRO HIS LEU VAL ALA VAL SEQRES 2 A 107 CYS PRO ILE PRO ALA ALA GLY LEU ASP VAL THR GLN PRO SEQRES 3 A 107 CYS GLY ASP CYS GLY THR ILE GLN GLU ASN TRP VAL CYS SEQRES 4 A 107 LEU SER CYS TYR GLN VAL TYR CYS GLY ARG TYR ILE ASN SEQRES 5 A 107 GLY HIS MET LEU GLN HIS HIS GLY ASN SER GLY HIS PRO SEQRES 6 A 107 LEU VAL LEU SER TYR ILE ASP LEU SER ALA TRP CYS TYR SEQRES 7 A 107 TYR CYS GLN ALA TYR VAL HIS HIS GLN ALA LEU LEU ASP SEQRES 8 A 107 VAL LYS ASN ILE ALA HIS GLN ASN LYS PHE GLY GLU ASP SEQRES 9 A 107 MET PRO HIS HET ZN A1301 1 HET ZN A1302 1 HET ZN A1303 1 HET FMT A1304 3 HET 6T5 A1305 18 HET UNX A1306 1 HET UNX A1307 1 HET UNX A1308 1 HET UNX A1309 1 HET UNX A1310 1 HET UNX A1311 1 HET UNX A1312 1 HET UNX A1313 1 HET UNX A1314 1 HET UNX A1315 1 HET UNX A1316 1 HET UNX A1317 1 HET UNX A1318 1 HET UNX A1319 1 HET UNX A1320 1 HET UNX A1321 1 HET UNX A1322 1 HET UNX A1323 1 HET UNX A1324 1 HET UNX A1325 1 HET UNX A1326 1 HET UNX A1327 1 HET UNX A1328 1 HET UNX A1329 1 HET UNX A1330 1 HET UNX A1331 1 HET UNX A1332 1 HET UNX A1333 1 HET UNX A1334 1 HET UNX A1335 1 HET UNX A1336 1 HET UNX A1337 1 HET UNX A1338 1 HET NA A1339 1 HETNAM ZN ZINC ION HETNAM FMT FORMIC ACID HETNAM 6T5 6-METHYL-5-[(4-PROPAN-2-YLPHENYL)AMINO]-2~{H}-1,2,4- HETNAM 2 6T5 TRIAZIN-3-ONE HETNAM UNX UNKNOWN ATOM OR ION HETNAM NA SODIUM ION FORMUL 2 ZN 3(ZN 2+) FORMUL 5 FMT C H2 O2 FORMUL 6 6T5 C13 H16 N4 O FORMUL 7 UNX 33(X) FORMUL 40 NA NA 1+ FORMUL 41 HOH *79(H2 O) HELIX 1 AA1 HIS A 1115 VAL A 1119 5 5 HELIX 2 AA2 GLY A 1159 GLY A 1169 1 11 HELIX 3 AA3 HIS A 1192 ALA A 1194 5 3 HELIX 4 AA4 LEU A 1195 GLY A 1208 1 14 SHEET 1 AA1 5 VAL A1151 CYS A1153 0 SHEET 2 AA1 5 ASN A1142 CYS A1145 -1 N TRP A1143 O TYR A1152 SHEET 3 AA1 5 LEU A1172 SER A1175 -1 O LEU A1174 N VAL A1144 SHEET 4 AA1 5 ALA A1181 CYS A1183 -1 O TRP A1182 N VAL A1173 SHEET 5 AA1 5 ALA A1188 TYR A1189 -1 O ALA A1188 N CYS A1183 LINK SG CYS A1113 ZN ZN A1303 1555 1555 2.34 LINK ND1 HIS A1115 ZN ZN A1303 1555 1555 2.14 LINK SG CYS A1133 ZN ZN A1302 1555 1555 2.37 LINK SG CYS A1136 ZN ZN A1302 1555 1555 2.35 LINK SG CYS A1145 ZN ZN A1301 1555 1555 2.30 LINK SG CYS A1153 ZN ZN A1302 1555 1555 2.36 LINK O TYR A1156 NA NA A1339 1555 1555 2.90 LINK O ILE A1157 NA NA A1339 1555 1555 2.40 LINK ND1 HIS A1160 ZN ZN A1302 1555 1555 2.12 LINK NE2 HIS A1164 ZN ZN A1301 1555 1555 2.08 LINK ND1 HIS A1170 ZN ZN A1301 1555 1555 2.07 LINK SG CYS A1183 ZN ZN A1303 1555 1555 2.34 LINK SG CYS A1186 ZN ZN A1303 1555 1555 2.53 LINK NA NA A1339 O HOH A1458 1555 1555 2.45 SITE 1 AC1 4 CYS A1145 CYS A1148 HIS A1164 HIS A1170 SITE 1 AC2 4 CYS A1133 CYS A1136 CYS A1153 HIS A1160 SITE 1 AC3 4 CYS A1113 HIS A1115 CYS A1183 CYS A1186 SITE 1 AC4 5 TRP A1143 GLY A1154 ARG A1155 TYR A1184 SITE 2 AC4 5 HOH A1422 SITE 1 AC5 6 TRP A1143 ARG A1155 TRP A1182 TYR A1189 SITE 2 AC5 6 ASN A1200 HOH A1447 SITE 1 AC6 3 TYR A1156 ILE A1157 HOH A1458 CRYST1 41.434 44.157 56.549 90.00 90.00 90.00 P 21 21 21 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 0.024135 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017684 0.00000