HEADER CELL CYCLE 18-MAR-16 5G0G TITLE CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 CD1 IN COMPLEX WITH TITLE 2 TRICHOSTATIN A COMPND MOL_ID: 1; COMPND 2 MOLECULE: HDAC6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN 1, UNP RESIDUES 40-418; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: POPINF KEYWDS CELL CYCLE, HISTONE, HISTONE DEACETYLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MIYAKE,J.J.KEUSCH,L.WANG,M.SAITO,D.HESS,X.WANG,B.J.MELANCON, AUTHOR 2 P.HELQUIST,H.GUT,P.MATTHIAS REVDAT 4 01-MAY-24 5G0G 1 REMARK LINK REVDAT 3 28-SEP-16 5G0G 1 JRNL REVDAT 2 10-AUG-16 5G0G 1 JRNL REVDAT 1 27-JUL-16 5G0G 0 JRNL AUTH Y.MIYAKE,J.J.KEUSCH,L.WANG,M.SAITO,D.HESS,X.WANG, JRNL AUTH 2 B.J.MELANCON,P.HELQUIST,H.GUT,P.MATTHIAS JRNL TITL STRUCTURAL INSIGHTS INTO HDAC6 TUBULIN DEACETYLATION AND ITS JRNL TITL 2 SELECTIVE INHIBITION JRNL REF NAT.CHEM.BIOL. V. 12 748 2016 JRNL REFN ISSN 1552-4450 JRNL PMID 27454931 JRNL DOI 10.1038/NCHEMBIO.2140 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 59655 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2983 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 46.5274 - 4.1360 0.99 2890 153 0.1346 0.1501 REMARK 3 2 4.1360 - 3.2831 0.98 2771 146 0.1311 0.1594 REMARK 3 3 3.2831 - 2.8682 0.99 2763 145 0.1510 0.1827 REMARK 3 4 2.8682 - 2.6059 0.99 2775 146 0.1450 0.1847 REMARK 3 5 2.6059 - 2.4192 0.99 2742 144 0.1381 0.1510 REMARK 3 6 2.4192 - 2.2766 1.00 2742 145 0.1308 0.1752 REMARK 3 7 2.2766 - 2.1625 0.99 2737 144 0.1253 0.1510 REMARK 3 8 2.1625 - 2.0684 0.97 2629 138 0.1223 0.1581 REMARK 3 9 2.0684 - 1.9888 0.98 2695 142 0.1219 0.1700 REMARK 3 10 1.9888 - 1.9201 0.99 2705 142 0.1196 0.1581 REMARK 3 11 1.9201 - 1.8601 0.99 2690 142 0.1197 0.1613 REMARK 3 12 1.8601 - 1.8069 0.98 2700 142 0.1197 0.1650 REMARK 3 13 1.8069 - 1.7594 0.99 2713 143 0.1312 0.1691 REMARK 3 14 1.7594 - 1.7164 0.99 2710 142 0.1383 0.1749 REMARK 3 15 1.7164 - 1.6774 0.98 2679 141 0.1526 0.2139 REMARK 3 16 1.6774 - 1.6417 0.98 2663 141 0.1674 0.2235 REMARK 3 17 1.6417 - 1.6089 0.98 2665 140 0.1848 0.2232 REMARK 3 18 1.6089 - 1.5785 0.98 2695 142 0.2049 0.2734 REMARK 3 19 1.5785 - 1.5503 0.98 2654 139 0.2178 0.2707 REMARK 3 20 1.5503 - 1.5240 0.96 2603 137 0.2521 0.2768 REMARK 3 21 1.5240 - 1.4995 0.90 2451 129 0.3208 0.3501 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.50 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 : 0.005 3062 REMARK 3 ANGLE : 0.791 4180 REMARK 3 CHIRALITY : 0.075 451 REMARK 3 PLANARITY : 0.005 567 REMARK 3 DIHEDRAL : 14.024 1136 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 5G0G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1290066424. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9780 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51661 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 1.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 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: HOMOLOGY MODEL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 3350, 0.2M MGCL2, 0.1M HEPES REMARK 280 PH 7.0, SB ADDITIVE A7 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 59.23500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.23500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 34.23500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.50500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.23500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.50500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.23500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.23500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.50500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.23500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.23500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.50500 REMARK 290 SMTRY3 8 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 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 A2083 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2093 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2156 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 GLY A 39 REMARK 465 PRO A 40 REMARK 465 ALA A 41 REMARK 465 GLU A 42 REMARK 465 GLU A 43 REMARK 465 GLU A 44 REMARK 465 MET A 45 REMARK 465 SER A 46 REMARK 465 ASN A 47 REMARK 465 GLU A 48 REMARK 465 LEU A 49 REMARK 465 GLN A 50 REMARK 465 ASN A 51 REMARK 465 LEU A 52 REMARK 465 ASP A 53 REMARK 465 VAL A 54 REMARK 465 GLN A 55 REMARK 465 GLY A 56 REMARK 465 LYS A 57 REMARK 465 SER A 58 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 ARG A 73 33.10 -98.24 REMARK 500 TYR A 255 -50.52 -135.85 REMARK 500 LEU A 303 -61.87 -128.82 REMARK 500 GLU A 360 -111.72 -111.83 REMARK 500 PRO A 388 -74.62 -67.81 REMARK 500 SER A 389 41.91 -76.49 REMARK 500 GLN A 416 55.74 -98.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2123 DISTANCE = 6.79 ANGSTROMS 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 NA A1421 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 228 OD1 REMARK 620 2 ASP A 228 O 73.1 REMARK 620 3 ASP A 230 O 98.9 105.8 REMARK 620 4 HIS A 232 O 90.7 163.0 81.4 REMARK 620 5 SER A 251 OG 104.0 85.3 156.7 93.9 REMARK 620 6 VAL A 252 O 151.0 81.8 73.9 115.2 87.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1419 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 230 OD2 REMARK 620 2 ASP A 230 OD1 57.1 REMARK 620 3 HIS A 232 ND1 152.9 95.9 REMARK 620 4 ASP A 323 OD2 91.0 107.2 95.5 REMARK 620 5 TSN A1427 O1 77.3 84.2 104.6 155.8 REMARK 620 6 TSN A1427 O2 121.0 163.3 85.4 89.1 79.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1420 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 241 O REMARK 620 2 ASP A 244 O 95.5 REMARK 620 3 VAL A 247 O 143.0 84.8 REMARK 620 4 HOH A2149 O 77.1 103.1 138.9 REMARK 620 5 HOH A2150 O 87.0 166.4 85.1 90.5 REMARK 620 N 1 2 3 4 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 1419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1421 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1423 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1424 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1425 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1426 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TSN A 1427 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5G0F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 ZNF-UBP DOMAIN REMARK 900 RELATED ID: 5G0H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 CD2 IN COMPLEX WITH (S)- REMARK 900 TRICHOSTATIN A REMARK 900 RELATED ID: 5G0I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 CD1 AND CD2 ( LINKER CLEAVED) REMARK 900 IN COMPLEX WITH NEXTURASTAT A REMARK 900 RELATED ID: 5G0J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 CD1 AND CD2 ( LINKER INTACT) REMARK 900 IN COMPLEX WITH NEXTURASTAT A DBREF 5G0G A 41 418 UNP F8W4B7 F8W4B7_DANRE 41 418 SEQADV 5G0G GLY A 39 UNP F8W4B7 EXPRESSION TAG SEQADV 5G0G PRO A 40 UNP F8W4B7 EXPRESSION TAG SEQRES 1 A 380 GLY PRO ALA GLU GLU GLU MET SER ASN GLU LEU GLN ASN SEQRES 2 A 380 LEU ASP VAL GLN GLY LYS SER LYS ALA THR GLY THR GLY SEQRES 3 A 380 LEU VAL TYR VAL ASP ALA PHE THR ARG PHE HIS CYS LEU SEQRES 4 A 380 TRP ASP ALA SER HIS PRO GLU CYS PRO ALA ARG VAL SER SEQRES 5 A 380 THR VAL MET GLU MET LEU GLU THR GLU GLY LEU LEU GLY SEQRES 6 A 380 ARG CYS VAL GLN VAL GLU ALA ARG ALA VAL THR GLU ASP SEQRES 7 A 380 GLU LEU LEU LEU VAL HIS THR LYS GLU TYR VAL GLU LEU SEQRES 8 A 380 MET LYS SER THR GLN ASN MET THR GLU GLU GLU LEU LYS SEQRES 9 A 380 THR LEU ALA GLU LYS TYR ASP SER VAL TYR LEU HIS PRO SEQRES 10 A 380 GLY PHE PHE SER SER ALA CYS LEU SER VAL GLY SER VAL SEQRES 11 A 380 LEU GLN LEU VAL ASP LYS VAL MET THR SER GLN LEU ARG SEQRES 12 A 380 ASN GLY PHE SER ILE ASN ARG PRO PRO GLY HIS HIS ALA SEQRES 13 A 380 GLN ALA ASP LYS MET ASN GLY PHE CYS MET PHE ASN ASN SEQRES 14 A 380 LEU ALA ILE ALA ALA ARG TYR ALA GLN LYS ARG HIS ARG SEQRES 15 A 380 VAL GLN ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS SEQRES 16 A 380 GLY GLN GLY ILE GLN TYR ILE PHE GLU GLU ASP PRO SER SEQRES 17 A 380 VAL LEU TYR PHE SER VAL HIS ARG TYR GLU ASP GLY SER SEQRES 18 A 380 PHE TRP PRO HIS LEU LYS GLU SER ASP SER SER SER VAL SEQRES 19 A 380 GLY SER GLY ALA GLY GLN GLY TYR ASN ILE ASN LEU PRO SEQRES 20 A 380 TRP ASN LYS VAL GLY MET GLU SER GLY ASP TYR ILE THR SEQRES 21 A 380 ALA PHE GLN GLN LEU LEU LEU PRO VAL ALA TYR GLU PHE SEQRES 22 A 380 GLN PRO GLN LEU VAL LEU VAL ALA ALA GLY PHE ASP ALA SEQRES 23 A 380 VAL ILE GLY ASP PRO LYS GLY GLY MET GLN VAL SER PRO SEQRES 24 A 380 GLU CYS PHE SER ILE LEU THR HIS MET LEU LYS GLY VAL SEQRES 25 A 380 ALA GLN GLY ARG LEU VAL LEU ALA LEU GLU GLY GLY TYR SEQRES 26 A 380 ASN LEU GLN SER THR ALA GLU GLY VAL CYS ALA SER MET SEQRES 27 A 380 ARG SER LEU LEU GLY ASP PRO CYS PRO HIS LEU PRO SER SEQRES 28 A 380 SER GLY ALA PRO CYS GLU SER ALA LEU LYS SER ILE SER SEQRES 29 A 380 LYS THR ILE SER ASP LEU TYR PRO PHE TRP LYS SER LEU SEQRES 30 A 380 GLN THR PHE HET ZN A1419 1 HET NA A1420 1 HET NA A1421 1 HET CL A1422 1 HET CL A1423 1 HET CL A1424 1 HET CL A1425 1 HET CL A1426 1 HET TSN A1427 22 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM TSN TRICHOSTATIN A HETSYN TSN 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7- HETSYN 2 TSN OXO-2,4-HEPTADIENAMIDE FORMUL 2 ZN ZN 2+ FORMUL 3 NA 2(NA 1+) FORMUL 5 CL 5(CL 1-) FORMUL 10 TSN C17 H22 N2 O3 FORMUL 11 HOH *250(H2 O) HELIX 1 1 VAL A 68 ARG A 73 5 6 HELIX 2 2 PRO A 86 GLU A 99 1 14 HELIX 3 3 LEU A 101 CYS A 105 5 5 HELIX 4 4 THR A 114 LEU A 119 1 6 HELIX 5 5 THR A 123 THR A 133 1 11 HELIX 6 6 GLN A 134 MET A 136 5 3 HELIX 7 7 THR A 137 GLU A 146 1 10 HELIX 8 8 GLY A 156 THR A 177 1 22 HELIX 9 9 ASN A 206 ARG A 220 1 15 HELIX 10 10 GLY A 234 GLU A 242 1 9 HELIX 11 11 GLU A 256 SER A 259 5 4 HELIX 12 12 LEU A 264 ASP A 268 5 5 HELIX 13 13 SER A 274 GLN A 278 5 5 HELIX 14 14 GLU A 292 LEU A 303 1 12 HELIX 15 15 LEU A 303 GLN A 312 1 10 HELIX 16 16 GLU A 338 LYS A 348 1 11 HELIX 17 17 GLY A 349 GLY A 353 5 5 HELIX 18 18 ASN A 364 LEU A 380 1 17 HELIX 19 19 CYS A 394 TYR A 409 1 16 HELIX 20 20 PRO A 410 GLN A 416 5 7 SHEET 1 AA 8 VAL A 106 GLN A 107 0 SHEET 2 AA 8 THR A 63 VAL A 66 1 O THR A 63 N VAL A 106 SHEET 3 AA 8 ASN A 182 SER A 185 1 O ASN A 182 N GLY A 64 SHEET 4 AA 8 LEU A 355 LEU A 359 1 O LEU A 355 N GLY A 183 SHEET 5 AA 8 LEU A 315 ALA A 320 1 O VAL A 316 N VAL A 356 SHEET 6 AA 8 VAL A 224 ASP A 228 1 O LEU A 225 N LEU A 317 SHEET 7 AA 8 VAL A 247 ARG A 254 1 O LEU A 248 N ILE A 226 SHEET 8 AA 8 ASN A 281 TRP A 286 1 O ILE A 282 N SER A 251 LINK OD1 ASP A 228 NA NA A1421 1555 1555 2.50 LINK O ASP A 228 NA NA A1421 1555 1555 2.73 LINK OD2 ASP A 230 ZN ZN A1419 1555 1555 2.45 LINK OD1 ASP A 230 ZN ZN A1419 1555 1555 2.05 LINK O ASP A 230 NA NA A1421 1555 1555 2.31 LINK ND1 HIS A 232 ZN ZN A1419 1555 1555 2.16 LINK O HIS A 232 NA NA A1421 1555 1555 2.58 LINK O PHE A 241 NA NA A1420 1555 1555 2.50 LINK O ASP A 244 NA NA A1420 1555 1555 2.28 LINK O VAL A 247 NA NA A1420 1555 1555 2.34 LINK OG SER A 251 NA NA A1421 1555 1555 2.61 LINK O VAL A 252 NA NA A1421 1555 1555 2.55 LINK OD2 ASP A 323 ZN ZN A1419 1555 1555 2.01 LINK ZN ZN A1419 O1 TSN A1427 1555 1555 2.00 LINK ZN ZN A1419 O2 TSN A1427 1555 1555 2.16 LINK NA NA A1420 O HOH A2149 1555 1555 2.35 LINK NA NA A1420 O HOH A2150 1555 1555 2.30 CISPEP 1 ARG A 188 PRO A 189 0 4.79 CISPEP 2 TRP A 261 PRO A 262 0 8.79 SITE 1 AC1 4 ASP A 230 HIS A 232 ASP A 323 TSN A1427 SITE 1 AC2 6 PHE A 241 ASP A 244 VAL A 247 TYR A 280 SITE 2 AC2 6 HOH A2149 HOH A2150 SITE 1 AC3 5 ASP A 228 ASP A 230 HIS A 232 SER A 251 SITE 2 AC3 5 VAL A 252 SITE 1 AC4 3 TRP A 78 LEU A 153 HOH A2017 SITE 1 AC5 2 ARG A 181 HOH A2215 SITE 1 AC6 5 SER A 293 SER A 336 PRO A 388 SER A 389 SITE 2 AC6 5 SER A 390 SITE 1 AC7 2 LYS A 174 GLN A 179 SITE 1 AC8 2 CYS A 394 GLU A 395 SITE 1 AC9 16 SER A 150 HIS A 192 HIS A 193 GLY A 201 SITE 2 AC9 16 PHE A 202 ASP A 230 HIS A 232 ASP A 257 SITE 3 AC9 16 GLY A 258 SER A 259 HIS A 263 LYS A 265 SITE 4 AC9 16 ASP A 323 LYS A 330 TYR A 363 ZN A1419 CRYST1 68.470 93.010 118.470 90.00 90.00 90.00 C 2 2 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 0.014605 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010752 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008441 0.00000