HEADER CELL CYCLE 18-MAR-16 5G0J TITLE CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 CD1 AND CD2 (LINKER INTACT) IN TITLE 2 COMPLEX WITH NEXTURASTAT A COMPND MOL_ID: 1; COMPND 2 MOLECULE: HDAC6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN 1 AND 2, UNP RESIDUES 40-831; 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_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: 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 10-JAN-24 5G0J 1 REMARK LINK REVDAT 3 28-SEP-16 5G0J 1 JRNL REVDAT 2 10-AUG-16 5G0J 1 JRNL REVDAT 1 27-JUL-16 5G0J 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. 2.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.5 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 47112 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2382 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.88 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.96 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3447 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2463 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3264 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE : 0.2708 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.31 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 183 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5860 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 88.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -21.98430 REMARK 3 B22 (A**2) : -21.98430 REMARK 3 B33 (A**2) : 43.96850 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) : 0.383 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.254 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.216 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.259 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.220 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.898 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.871 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 6038 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 8196 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2053 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 135 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 909 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 6038 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 5 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 765 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 1 ; 1.000 ; HARMONIC REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 7316 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.22 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.99 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.99 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DIFFRACTION DATA ARE ANISOTROPIC. REMARK 3 STRUCTURAL MODELING WAS CARRIED OUT USING MAP SHARPENING REMARK 4 REMARK 4 5G0J 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_1290066479. 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 : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47289 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.880 REMARK 200 RESOLUTION RANGE LOW (A) : 162.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.30 REMARK 200 R MERGE FOR SHELL (I) : 0.79000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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 ENTRIES 5G0G AND 5G0H REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 78.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.3M SODIUM FORMATE, 17% GLYCEROL, REMARK 280 0.1M TRIS PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 68.47867 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 34.23933 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 34.23933 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 68.47867 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 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 38 REMARK 465 PRO A 39 REMARK 465 LYS 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 PRO A 810 REMARK 465 SER A 811 REMARK 465 PRO A 812 REMARK 465 LYS A 813 REMARK 465 PRO A 814 REMARK 465 LYS A 815 REMARK 465 GLY A 816 REMARK 465 LYS A 817 REMARK 465 CYS A 818 REMARK 465 THR A 819 REMARK 465 PRO A 820 REMARK 465 GLY A 821 REMARK 465 GLY A 822 REMARK 465 LYS A 823 REMARK 465 GLY A 824 REMARK 465 LYS A 825 REMARK 465 LYS A 826 REMARK 465 SER A 827 REMARK 465 PRO A 828 REMARK 465 ARG A 829 REMARK 465 GLN A 830 REMARK 465 SER A 831 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 VAL A 121 -36.35 -133.83 REMARK 500 ASN A 200 138.49 -172.27 REMARK 500 MET A 204 -62.03 -100.53 REMARK 500 LYS A 217 -71.91 -73.94 REMARK 500 GLN A 222 -74.26 -77.72 REMARK 500 TYR A 255 -56.05 -131.21 REMARK 500 TYR A 280 40.42 -105.94 REMARK 500 GLU A 292 -167.22 -116.70 REMARK 500 LEU A 303 -62.73 -121.31 REMARK 500 GLN A 312 70.42 47.74 REMARK 500 GLU A 338 -31.57 -39.98 REMARK 500 ALA A 351 14.27 56.39 REMARK 500 ARG A 354 95.39 -65.82 REMARK 500 GLU A 360 -104.67 -112.95 REMARK 500 SER A 424 154.89 -46.25 REMARK 500 MET A 458 3.91 -65.65 REMARK 500 TRP A 459 -66.09 -124.67 REMARK 500 PRO A 571 -177.97 -63.34 REMARK 500 PHE A 583 -2.23 79.43 REMARK 500 THR A 600 -101.61 -109.09 REMARK 500 PRO A 644 30.87 -85.59 REMARK 500 ASN A 645 10.61 59.50 REMARK 500 LEU A 685 -59.55 -126.22 REMARK 500 ALA A 694 77.77 57.25 REMARK 500 GLN A 716 53.69 -110.27 REMARK 500 GLU A 742 -98.17 -114.03 REMARK 500 ASP A 770 -155.53 -79.78 REMARK 500 ARG A 798 77.17 -51.87 REMARK 500 VAL A 799 76.38 -103.70 REMARK 500 PRO A 802 -122.91 -78.47 REMARK 500 ARG A 806 1.37 -58.83 REMARK 500 SER A 808 156.47 58.36 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 A2020 DISTANCE = 6.30 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 K A1814 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 228 O REMARK 620 2 ASP A 228 OD1 69.4 REMARK 620 3 ASP A 230 O 91.0 94.8 REMARK 620 4 HIS A 232 O 154.2 85.5 85.2 REMARK 620 5 SER A 251 OG 86.8 97.9 165.4 102.9 REMARK 620 6 VAL A 252 O 72.0 136.6 66.7 128.4 99.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1812 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 230 OD2 REMARK 620 2 ASP A 230 OD1 49.3 REMARK 620 3 HIS A 232 ND1 122.3 73.8 REMARK 620 4 ASP A 323 OD2 81.7 72.7 72.2 REMARK 620 5 TYR A 363 OH 124.1 157.8 104.4 85.5 REMARK 620 6 HOH A2060 O 94.4 137.4 141.3 130.5 56.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1815 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 241 O REMARK 620 2 ASP A 244 O 81.5 REMARK 620 3 VAL A 247 O 121.3 76.4 REMARK 620 4 TYR A 280 O 134.8 141.2 90.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1816 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 ASP A 610 O 79.8 REMARK 620 3 ASP A 612 O 97.2 101.1 REMARK 620 4 HIS A 614 O 76.9 155.6 75.1 REMARK 620 5 SER A 633 OG 85.6 82.8 175.5 102.3 REMARK 620 6 LEU A 634 O 151.3 82.2 64.5 115.9 114.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1811 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 612 OD1 REMARK 620 2 HIS A 614 ND1 103.2 REMARK 620 3 ASP A 705 OD2 86.5 76.7 REMARK 620 4 N4R A1817 O 168.7 85.4 102.8 REMARK 620 5 HOH A2141 O 87.0 80.0 153.7 87.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1813 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 623 O REMARK 620 2 ASP A 626 O 73.8 REMARK 620 3 VAL A 629 O 107.7 73.2 REMARK 620 4 TYR A 662 O 142.0 144.0 87.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1809 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1811 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1812 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1813 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1814 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1815 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1816 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE N4R A 1817 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: 5G0G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 CD1 IN COMPLEX WITH REMARK 900 TRICHOSTATIN A 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 DBREF 5G0J A 40 831 UNP F8W4B7 F8W4B7_DANRE 40 831 SEQADV 5G0J GLY A 38 UNP F8W4B7 EXPRESSION TAG SEQADV 5G0J PRO A 39 UNP F8W4B7 EXPRESSION TAG SEQRES 1 A 794 GLY PRO LYS ALA GLU GLU GLU MET SER ASN GLU LEU GLN SEQRES 2 A 794 ASN LEU ASP VAL GLN GLY LYS SER LYS ALA THR GLY THR SEQRES 3 A 794 GLY LEU VAL TYR VAL ASP ALA PHE THR ARG PHE HIS CYS SEQRES 4 A 794 LEU TRP ASP ALA SER HIS PRO GLU CYS PRO ALA ARG VAL SEQRES 5 A 794 SER THR VAL MET GLU MET LEU GLU THR GLU GLY LEU LEU SEQRES 6 A 794 GLY ARG CYS VAL GLN VAL GLU ALA ARG ALA VAL THR GLU SEQRES 7 A 794 ASP GLU LEU LEU LEU VAL HIS THR LYS GLU TYR VAL GLU SEQRES 8 A 794 LEU MET LYS SER THR GLN ASN MET THR GLU GLU GLU LEU SEQRES 9 A 794 LYS THR LEU ALA GLU LYS TYR ASP SER VAL TYR LEU HIS SEQRES 10 A 794 PRO GLY PHE PHE SER SER ALA CYS LEU SER VAL GLY SER SEQRES 11 A 794 VAL LEU GLN LEU VAL ASP LYS VAL MET THR SER GLN LEU SEQRES 12 A 794 ARG ASN GLY PHE SER ILE ASN ARG PRO PRO GLY HIS HIS SEQRES 13 A 794 ALA GLN ALA ASP LYS MET ASN GLY PHE CYS MET PHE ASN SEQRES 14 A 794 ASN LEU ALA ILE ALA ALA ARG TYR ALA GLN LYS ARG HIS SEQRES 15 A 794 ARG VAL GLN ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS SEQRES 16 A 794 HIS GLY GLN GLY ILE GLN TYR ILE PHE GLU GLU ASP PRO SEQRES 17 A 794 SER VAL LEU TYR PHE SER VAL HIS ARG TYR GLU ASP GLY SEQRES 18 A 794 SER PHE TRP PRO HIS LEU LYS GLU SER ASP SER SER SER SEQRES 19 A 794 VAL GLY SER GLY ALA GLY GLN GLY TYR ASN ILE ASN LEU SEQRES 20 A 794 PRO TRP ASN LYS VAL GLY MET GLU SER GLY ASP TYR ILE SEQRES 21 A 794 THR ALA PHE GLN GLN LEU LEU LEU PRO VAL ALA TYR GLU SEQRES 22 A 794 PHE GLN PRO GLN LEU VAL LEU VAL ALA ALA GLY PHE ASP SEQRES 23 A 794 ALA VAL ILE GLY ASP PRO LYS GLY GLY MET GLN VAL SER SEQRES 24 A 794 PRO GLU CYS PHE SER ILE LEU THR HIS MET LEU LYS GLY SEQRES 25 A 794 VAL ALA GLN GLY ARG LEU VAL LEU ALA LEU GLU GLY GLY SEQRES 26 A 794 TYR ASN LEU GLN SER THR ALA GLU GLY VAL CYS ALA SER SEQRES 27 A 794 MET ARG SER LEU LEU GLY ASP PRO CYS PRO HIS LEU PRO SEQRES 28 A 794 SER SER GLY ALA PRO CYS GLU SER ALA LEU LYS SER ILE SEQRES 29 A 794 SER LYS THR ILE SER ASP LEU TYR PRO PHE TRP LYS SER SEQRES 30 A 794 LEU GLN THR PHE GLU GLY GLY PRO LEU SER GLU VAL SER SEQRES 31 A 794 PRO LEU PRO ALA PRO VAL CYS ALA GLU VAL LYS VAL SER SEQRES 32 A 794 SER PRO ILE THR GLY LEU VAL TYR ASP GLN ARG MET MET SEQRES 33 A 794 LEU HIS HIS ASN MET TRP ASP SER HIS HIS PRO GLU LEU SEQRES 34 A 794 PRO GLN ARG ILE SER ARG ILE PHE SER ARG HIS GLU GLU SEQRES 35 A 794 LEU ARG LEU LEU SER ARG CYS HIS ARG ILE PRO ALA ARG SEQRES 36 A 794 LEU ALA THR GLU GLU GLU LEU ALA LEU CYS HIS SER SER SEQRES 37 A 794 LYS HIS ILE SER ILE ILE LYS SER SER GLU HIS MET LYS SEQRES 38 A 794 PRO ARG ASP LEU ASN ARG LEU GLY ASP GLU TYR ASN SER SEQRES 39 A 794 ILE PHE ILE SER ASN GLU SER TYR THR CYS ALA LEU LEU SEQRES 40 A 794 ALA ALA GLY SER CYS PHE ASN SER ALA GLN ALA ILE LEU SEQRES 41 A 794 THR GLY GLN VAL ARG ASN ALA VAL ALA ILE VAL ARG PRO SEQRES 42 A 794 PRO GLY HIS HIS ALA GLU LYS ASP THR ALA CYS GLY PHE SEQRES 43 A 794 CYS PHE PHE ASN THR ALA ALA LEU THR ALA ARG TYR ALA SEQRES 44 A 794 GLN SER ILE THR ARG GLU SER LEU ARG VAL LEU ILE VAL SEQRES 45 A 794 ASP TRP ASP VAL HIS HIS GLY ASN GLY THR GLN HIS ILE SEQRES 46 A 794 PHE GLU GLU ASP ASP SER VAL LEU TYR ILE SER LEU HIS SEQRES 47 A 794 ARG TYR GLU ASP GLY ALA PHE PHE PRO ASN SER GLU ASP SEQRES 48 A 794 ALA ASN TYR ASP LYS VAL GLY LEU GLY LYS GLY ARG GLY SEQRES 49 A 794 TYR ASN VAL ASN ILE PRO TRP ASN GLY GLY LYS MET GLY SEQRES 50 A 794 ASP PRO GLU TYR MET ALA ALA PHE HIS HIS LEU VAL MET SEQRES 51 A 794 PRO ILE ALA ARG GLU PHE ALA PRO GLU LEU VAL LEU VAL SEQRES 52 A 794 SER ALA GLY PHE ASP ALA ALA ARG GLY ASP PRO LEU GLY SEQRES 53 A 794 GLY PHE GLN VAL THR PRO GLU GLY TYR ALA HIS LEU THR SEQRES 54 A 794 HIS GLN LEU MET SER LEU ALA ALA GLY ARG VAL LEU ILE SEQRES 55 A 794 ILE LEU GLU GLY GLY TYR ASN LEU THR SER ILE SER GLU SEQRES 56 A 794 SER MET SER MET CYS THR SER MET LEU LEU GLY ASP SER SEQRES 57 A 794 PRO PRO SER LEU ASP HIS LEU THR PRO LEU LYS THR SER SEQRES 58 A 794 ALA THR VAL SER ILE ASN ASN VAL LEU ARG ALA HIS ALA SEQRES 59 A 794 PRO PHE TRP SER SER LEU ARG VAL ASN ILE PRO GLU SER SEQRES 60 A 794 LEU ARG LEU SER LEU PRO SER PRO LYS PRO LYS GLY LYS SEQRES 61 A 794 CYS THR PRO GLY GLY LYS GLY LYS LYS SER PRO ARG GLN SEQRES 62 A 794 SER HET CL A1809 1 HET CL A1810 1 HET ZN A1811 1 HET K A1812 1 HET K A1813 1 HET K A1814 1 HET K A1815 1 HET K A1816 1 HET N4R A1817 25 HETNAM CL CHLORIDE ION HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM N4R NEXTURASTAT A FORMUL 2 CL 2(CL 1-) FORMUL 4 ZN ZN 2+ FORMUL 5 K 5(K 1+) FORMUL 10 N4R C19 H23 N3 O3 FORMUL 11 HOH *162(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 LYS A 147 1 11 HELIX 8 8 GLY A 156 THR A 177 1 22 HELIX 9 9 ASN A 206 HIS A 219 1 14 HELIX 10 10 GLY A 234 PHE A 241 1 8 HELIX 11 11 SER A 274 GLN A 278 5 5 HELIX 12 12 GLU A 292 LEU A 303 1 12 HELIX 13 13 LEU A 303 GLN A 312 1 10 HELIX 14 14 PRO A 337 VAL A 350 1 14 HELIX 15 15 ALA A 351 GLY A 353 5 3 HELIX 16 16 ASN A 364 LEU A 380 1 17 HELIX 17 17 CYS A 394 TYR A 409 1 16 HELIX 18 18 SER A 414 PHE A 418 5 5 HELIX 19 19 ASP A 449 LEU A 454 5 6 HELIX 20 20 PRO A 467 LEU A 480 1 14 HELIX 21 21 LEU A 482 CYS A 486 5 5 HELIX 22 22 THR A 495 LEU A 501 1 7 HELIX 23 23 SER A 504 SER A 514 1 11 HELIX 24 24 LYS A 518 GLU A 528 1 11 HELIX 25 25 GLU A 537 THR A 558 1 22 HELIX 26 26 ASN A 587 THR A 600 1 14 HELIX 27 27 GLY A 616 PHE A 623 1 8 HELIX 28 28 GLU A 638 ALA A 641 5 4 HELIX 29 29 SER A 646 ASN A 650 5 5 HELIX 30 30 LEU A 656 ARG A 660 5 5 HELIX 31 31 GLY A 674 LEU A 685 1 12 HELIX 32 32 LEU A 685 ALA A 694 1 10 HELIX 33 33 THR A 718 MET A 730 1 13 HELIX 34 34 SER A 731 GLY A 735 5 5 HELIX 35 35 ASN A 746 LEU A 762 1 17 HELIX 36 36 LYS A 776 ALA A 791 1 16 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 SHEET 1 AB 8 HIS A 487 ARG A 488 0 SHEET 2 AB 8 THR A 444 VAL A 447 1 O THR A 444 N HIS A 487 SHEET 3 AB 8 ASN A 563 ALA A 566 1 O ASN A 563 N GLY A 445 SHEET 4 AB 8 VAL A 737 LEU A 741 1 O VAL A 737 N ALA A 564 SHEET 5 AB 8 LEU A 697 ALA A 702 1 O VAL A 698 N LEU A 738 SHEET 6 AB 8 VAL A 606 ASP A 610 1 O LEU A 607 N LEU A 699 SHEET 7 AB 8 VAL A 629 ARG A 636 1 O LEU A 630 N ILE A 608 SHEET 8 AB 8 ASN A 663 TRP A 668 1 O VAL A 664 N SER A 633 LINK O ASP A 228 K K A1814 1555 1555 2.92 LINK OD1 ASP A 228 K K A1814 1555 1555 2.36 LINK OD2 ASP A 230 K K A1812 1555 1555 2.63 LINK OD1 ASP A 230 K K A1812 1555 1555 2.66 LINK O ASP A 230 K K A1814 1555 1555 2.56 LINK ND1 HIS A 232 K K A1812 1555 1555 3.04 LINK O HIS A 232 K K A1814 1555 1555 2.63 LINK O PHE A 241 K K A1815 1555 1555 2.35 LINK O ASP A 244 K K A1815 1555 1555 2.67 LINK O VAL A 247 K K A1815 1555 1555 2.63 LINK OG SER A 251 K K A1814 1555 1555 2.84 LINK O VAL A 252 K K A1814 1555 1555 2.82 LINK O TYR A 280 K K A1815 1555 1555 2.43 LINK OD2 ASP A 323 K K A1812 1555 1555 2.75 LINK OH TYR A 363 K K A1812 1555 1555 3.00 LINK OD1 ASP A 610 K K A1816 1555 1555 2.77 LINK O ASP A 610 K K A1816 1555 1555 3.01 LINK OD1 ASP A 612 ZN ZN A1811 1555 1555 2.04 LINK O ASP A 612 K K A1816 1555 1555 2.62 LINK ND1 HIS A 614 ZN ZN A1811 1555 1555 2.46 LINK O HIS A 614 K K A1816 1555 1555 2.95 LINK O PHE A 623 K K A1813 1555 1555 2.78 LINK O ASP A 626 K K A1813 1555 1555 2.50 LINK O VAL A 629 K K A1813 1555 1555 2.89 LINK OG SER A 633 K K A1816 1555 1555 2.84 LINK O LEU A 634 K K A1816 1555 1555 2.58 LINK O TYR A 662 K K A1813 1555 1555 2.36 LINK OD2 ASP A 705 ZN ZN A1811 1555 1555 2.07 LINK ZN ZN A1811 O N4R A1817 1555 1555 1.99 LINK ZN ZN A1811 O HOH A2141 1555 1555 1.89 LINK K K A1812 O HOH A2060 1555 1555 2.58 CISPEP 1 ARG A 188 PRO A 189 0 10.21 CISPEP 2 TRP A 261 PRO A 262 0 5.19 CISPEP 3 ARG A 569 PRO A 570 0 3.58 CISPEP 4 PHE A 643 PRO A 644 0 0.91 CISPEP 5 THR A 773 PRO A 774 0 6.52 SITE 1 AC1 2 ASP A 257 CYS A 486 SITE 1 AC2 4 GLN A 416 GLU A 419 THR A 780 LEU A 805 SITE 1 AC3 5 ASP A 612 HIS A 614 ASP A 705 N4R A1817 SITE 2 AC3 5 HOH A2141 SITE 1 AC4 8 LYS A 57 HIS A 192 ASP A 230 HIS A 232 SITE 2 AC4 8 ASP A 323 GLY A 361 TYR A 363 HOH A2060 SITE 1 AC5 4 PHE A 623 ASP A 626 VAL A 629 TYR A 662 SITE 1 AC6 6 ASP A 228 ASP A 230 HIS A 232 SER A 251 SITE 2 AC6 6 VAL A 252 HIS A 253 SITE 1 AC7 4 PHE A 241 ASP A 244 VAL A 247 TYR A 280 SITE 1 AC8 5 ASP A 610 ASP A 612 HIS A 614 SER A 633 SITE 2 AC8 5 LEU A 634 SITE 1 AC9 15 HIS A 463 PRO A 464 SER A 531 HIS A 573 SITE 2 AC9 15 HIS A 574 GLY A 582 PHE A 583 ASP A 612 SITE 3 AC9 15 HIS A 614 PHE A 643 ASP A 705 LEU A 712 SITE 4 AC9 15 TYR A 745 ZN A1811 HOH A2141 CRYST1 187.224 187.224 102.718 90.00 90.00 120.00 P 32 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 0.005341 0.003084 0.000000 0.00000 SCALE2 0.000000 0.006167 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009735 0.00000