HEADER HYDROLASE/HYDROLASE INHIBITOR 23-OCT-15 5EF8 TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATALYTIC TITLE 2 DOMAIN 2 IN COMPLEX WITH PANOBINOSTAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HDAC6 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN 2 (UNP RESIDUES 288-646); COMPND 5 SYNONYM: HISTONE DEACETYLASE 6; COMPND 6 EC: 3.5.1.98; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: HDAC6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.HAI,D.W.CHRISTIANSON REVDAT 6 27-SEP-23 5EF8 1 LINK REVDAT 5 25-DEC-19 5EF8 1 REMARK REVDAT 4 13-SEP-17 5EF8 1 REMARK REVDAT 3 07-SEP-16 5EF8 1 JRNL REVDAT 2 10-AUG-16 5EF8 1 JRNL REVDAT 1 27-JUL-16 5EF8 0 JRNL AUTH Y.HAI,D.W.CHRISTIANSON JRNL TITL HISTONE DEACETYLASE 6 STRUCTURE AND MOLECULAR BASIS OF JRNL TITL 2 CATALYSIS AND INHIBITION. JRNL REF NAT.CHEM.BIOL. V. 12 741 2016 JRNL REFN ESSN 1552-4469 JRNL PMID 27454933 JRNL DOI 10.1038/NCHEMBIO.2134 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.3_1479 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 26470 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1325 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 49.7168 - 5.3955 0.99 2980 158 0.1487 0.1791 REMARK 3 2 5.3955 - 4.2833 1.00 2875 152 0.1481 0.2016 REMARK 3 3 4.2833 - 3.7421 1.00 2833 149 0.1697 0.2257 REMARK 3 4 3.7421 - 3.4000 1.00 2807 148 0.1837 0.2251 REMARK 3 5 3.4000 - 3.1564 1.00 2809 147 0.2084 0.2685 REMARK 3 6 3.1564 - 2.9703 1.00 2780 147 0.2210 0.2349 REMARK 3 7 2.9703 - 2.8216 1.00 2788 146 0.2232 0.2817 REMARK 3 8 2.8216 - 2.6988 0.99 2749 145 0.2443 0.2714 REMARK 3 9 2.6988 - 2.5949 0.90 2524 133 0.2642 0.3253 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.002 5819 REMARK 3 ANGLE : 0.713 7901 REMARK 3 CHIRALITY : 0.026 855 REMARK 3 PLANARITY : 0.004 1028 REMARK 3 DIHEDRAL : 12.707 2123 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 5EF8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214813. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26544 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.21700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.69900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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 5EEK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 6.5, 12% PEG20000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 32.58400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 70.19800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.58400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 70.19800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 A2181 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 SER A 435 REMARK 465 ASN A 436 REMARK 465 ALA A 437 REMARK 465 GLY A 438 REMARK 465 GLY A 439 REMARK 465 SER A 440 REMARK 465 SER A 441 REMARK 465 SER B 435 REMARK 465 ASN B 436 REMARK 465 ALA B 437 REMARK 465 GLY B 438 REMARK 465 GLY B 439 REMARK 465 SER B 440 REMARK 465 SER B 441 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 ARG A 524 CD NE CZ NH1 NH2 REMARK 470 ARG B 524 CD NE CZ NH1 NH2 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 OH TYR B 745 O1 LBH B 2004 2.13 REMARK 500 OH TYR A 745 O1 LBH A 2004 2.17 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 PRO A 571 -175.98 -63.92 REMARK 500 THR A 600 -95.61 -134.47 REMARK 500 TYR A 637 -53.46 -126.29 REMARK 500 LEU A 685 -68.38 -124.85 REMARK 500 ALA A 694 71.39 50.75 REMARK 500 GLN A 716 38.38 -142.66 REMARK 500 ARG A 736 82.37 -68.82 REMARK 500 GLU A 742 -104.20 -117.25 REMARK 500 ASP B 460 94.40 -162.97 REMARK 500 THR B 600 -88.62 -126.68 REMARK 500 ALA B 641 41.86 -94.17 REMARK 500 LEU B 685 -67.30 -122.71 REMARK 500 ALA B 694 71.43 52.88 REMARK 500 SER B 701 80.99 -69.93 REMARK 500 GLN B 716 44.89 -146.08 REMARK 500 GLU B 742 -105.13 -115.23 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 A2002 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 O REMARK 620 2 ASP A 610 OD1 74.1 REMARK 620 3 ASP A 612 O 100.9 94.9 REMARK 620 4 HIS A 614 O 165.6 94.4 71.0 REMARK 620 5 SER A 633 OG 84.6 115.4 149.4 108.5 REMARK 620 6 LEU A 634 O 74.4 136.7 63.1 110.5 90.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 612 OD1 REMARK 620 2 ASP A 612 OD2 52.0 REMARK 620 3 HIS A 614 ND1 97.5 144.0 REMARK 620 4 ASP A 705 OD2 102.4 77.6 93.9 REMARK 620 5 LBH A2004 O2 89.8 78.3 125.6 137.0 REMARK 620 6 LBH A2004 N3 106.2 114.6 90.1 150.3 37.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A2003 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 623 O REMARK 620 2 ASP A 626 O 72.2 REMARK 620 3 VAL A 629 O 110.5 77.7 REMARK 620 4 TYR A 662 O 158.2 117.5 91.0 REMARK 620 5 HOH A2116 O 68.1 139.5 123.9 97.5 REMARK 620 6 HOH A2122 O 74.0 84.7 159.0 87.1 77.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B2002 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 610 O REMARK 620 2 ASP B 610 OD1 76.5 REMARK 620 3 ASP B 612 O 95.2 98.7 REMARK 620 4 HIS B 614 O 166.4 95.2 75.2 REMARK 620 5 SER B 633 OG 82.8 116.3 143.1 110.7 REMARK 620 6 LEU B 634 O 70.3 138.0 60.5 111.7 84.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 612 OD1 REMARK 620 2 HIS B 614 ND1 106.2 REMARK 620 3 ASP B 705 OD2 96.8 101.4 REMARK 620 4 LBH B2004 O1 153.4 92.4 97.9 REMARK 620 5 LBH B2004 O2 84.7 111.4 145.4 70.6 REMARK 620 6 LBH B2004 N3 108.5 84.5 151.3 53.5 31.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B2003 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 623 O REMARK 620 2 ASP B 626 O 75.5 REMARK 620 3 VAL B 629 O 121.3 86.4 REMARK 620 4 TYR B 662 O 149.1 117.2 88.7 REMARK 620 5 HOH B2109 O 77.8 80.0 153.0 77.2 REMARK 620 6 HOH B2124 O 70.6 143.5 122.8 87.4 80.0 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 ZN A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 2003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LBH A 2004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 2005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 2003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LBH B 2004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 2005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 2006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 2007 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EDU RELATED DB: PDB REMARK 900 RELATED ID: 5EEF RELATED DB: PDB REMARK 900 RELATED ID: 5EEI RELATED DB: PDB REMARK 900 RELATED ID: 5EEK RELATED DB: PDB REMARK 900 RELATED ID: 5EEM RELATED DB: PDB REMARK 900 RELATED ID: 5EEN RELATED DB: PDB REMARK 900 RELATED ID: 5EF7 RELATED DB: PDB REMARK 900 RELATED ID: 5EFB RELATED DB: PDB REMARK 900 RELATED ID: 5EFG RELATED DB: PDB REMARK 900 RELATED ID: 5EFH RELATED DB: PDB REMARK 900 RELATED ID: 5EFJ RELATED DB: PDB REMARK 900 RELATED ID: 5EFK RELATED DB: PDB REMARK 900 RELATED ID: 5EFN RELATED DB: PDB DBREF 5EF8 A 440 798 UNP A7YT55 A7YT55_DANRE 288 646 DBREF 5EF8 B 440 798 UNP A7YT55 A7YT55_DANRE 288 646 SEQADV 5EF8 SER A 435 UNP A7YT55 EXPRESSION TAG SEQADV 5EF8 ASN A 436 UNP A7YT55 EXPRESSION TAG SEQADV 5EF8 ALA A 437 UNP A7YT55 EXPRESSION TAG SEQADV 5EF8 GLY A 438 UNP A7YT55 EXPRESSION TAG SEQADV 5EF8 GLY A 439 UNP A7YT55 EXPRESSION TAG SEQADV 5EF8 SER B 435 UNP A7YT55 EXPRESSION TAG SEQADV 5EF8 ASN B 436 UNP A7YT55 EXPRESSION TAG SEQADV 5EF8 ALA B 437 UNP A7YT55 EXPRESSION TAG SEQADV 5EF8 GLY B 438 UNP A7YT55 EXPRESSION TAG SEQADV 5EF8 GLY B 439 UNP A7YT55 EXPRESSION TAG SEQRES 1 A 364 SER ASN ALA GLY GLY SER SER PRO ILE THR GLY LEU VAL SEQRES 2 A 364 TYR ASP GLN ARG MET MET LEU HIS HIS ASN MET TRP ASP SEQRES 3 A 364 SER HIS HIS PRO GLU LEU PRO GLN ARG ILE SER ARG ILE SEQRES 4 A 364 PHE SER ARG HIS GLU GLU LEU ARG LEU LEU SER ARG CYS SEQRES 5 A 364 HIS ARG ILE PRO ALA ARG LEU ALA THR GLU GLU GLU LEU SEQRES 6 A 364 ALA LEU CYS HIS SER SER LYS HIS ILE SER ILE ILE LYS SEQRES 7 A 364 SER SER GLU HIS MET LYS PRO ARG ASP LEU ASN ARG LEU SEQRES 8 A 364 GLY ASP GLU TYR ASN SER ILE PHE ILE SER ASN GLU SER SEQRES 9 A 364 TYR THR CYS ALA LEU LEU ALA ALA GLY SER CYS PHE ASN SEQRES 10 A 364 SER ALA GLN ALA ILE LEU THR GLY GLN VAL ARG ASN ALA SEQRES 11 A 364 VAL ALA ILE VAL ARG PRO PRO GLY HIS HIS ALA GLU LYS SEQRES 12 A 364 ASP THR ALA CYS GLY PHE CYS PHE PHE ASN THR ALA ALA SEQRES 13 A 364 LEU THR ALA ARG TYR ALA GLN SER ILE THR ARG GLU SER SEQRES 14 A 364 LEU ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS GLY SEQRES 15 A 364 ASN GLY THR GLN HIS ILE PHE GLU GLU ASP ASP SER VAL SEQRES 16 A 364 LEU TYR ILE SER LEU HIS ARG TYR GLU ASP GLY ALA PHE SEQRES 17 A 364 PHE PRO ASN SER GLU ASP ALA ASN TYR ASP LYS VAL GLY SEQRES 18 A 364 LEU GLY LYS GLY ARG GLY TYR ASN VAL ASN ILE PRO TRP SEQRES 19 A 364 ASN GLY GLY LYS MET GLY ASP PRO GLU TYR MET ALA ALA SEQRES 20 A 364 PHE HIS HIS LEU VAL MET PRO ILE ALA ARG GLU PHE ALA SEQRES 21 A 364 PRO GLU LEU VAL LEU VAL SER ALA GLY PHE ASP ALA ALA SEQRES 22 A 364 ARG GLY ASP PRO LEU GLY GLY PHE GLN VAL THR PRO GLU SEQRES 23 A 364 GLY TYR ALA HIS LEU THR HIS GLN LEU MET SER LEU ALA SEQRES 24 A 364 ALA GLY ARG VAL LEU ILE ILE LEU GLU GLY GLY TYR ASN SEQRES 25 A 364 LEU THR SER ILE SER GLU SER MET SER MET CYS THR SER SEQRES 26 A 364 MET LEU LEU GLY ASP SER PRO PRO SER LEU ASP HIS LEU SEQRES 27 A 364 THR PRO LEU LYS THR SER ALA THR VAL SER ILE ASN ASN SEQRES 28 A 364 VAL LEU ARG ALA HIS ALA PRO PHE TRP SER SER LEU ARG SEQRES 1 B 364 SER ASN ALA GLY GLY SER SER PRO ILE THR GLY LEU VAL SEQRES 2 B 364 TYR ASP GLN ARG MET MET LEU HIS HIS ASN MET TRP ASP SEQRES 3 B 364 SER HIS HIS PRO GLU LEU PRO GLN ARG ILE SER ARG ILE SEQRES 4 B 364 PHE SER ARG HIS GLU GLU LEU ARG LEU LEU SER ARG CYS SEQRES 5 B 364 HIS ARG ILE PRO ALA ARG LEU ALA THR GLU GLU GLU LEU SEQRES 6 B 364 ALA LEU CYS HIS SER SER LYS HIS ILE SER ILE ILE LYS SEQRES 7 B 364 SER SER GLU HIS MET LYS PRO ARG ASP LEU ASN ARG LEU SEQRES 8 B 364 GLY ASP GLU TYR ASN SER ILE PHE ILE SER ASN GLU SER SEQRES 9 B 364 TYR THR CYS ALA LEU LEU ALA ALA GLY SER CYS PHE ASN SEQRES 10 B 364 SER ALA GLN ALA ILE LEU THR GLY GLN VAL ARG ASN ALA SEQRES 11 B 364 VAL ALA ILE VAL ARG PRO PRO GLY HIS HIS ALA GLU LYS SEQRES 12 B 364 ASP THR ALA CYS GLY PHE CYS PHE PHE ASN THR ALA ALA SEQRES 13 B 364 LEU THR ALA ARG TYR ALA GLN SER ILE THR ARG GLU SER SEQRES 14 B 364 LEU ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS GLY SEQRES 15 B 364 ASN GLY THR GLN HIS ILE PHE GLU GLU ASP ASP SER VAL SEQRES 16 B 364 LEU TYR ILE SER LEU HIS ARG TYR GLU ASP GLY ALA PHE SEQRES 17 B 364 PHE PRO ASN SER GLU ASP ALA ASN TYR ASP LYS VAL GLY SEQRES 18 B 364 LEU GLY LYS GLY ARG GLY TYR ASN VAL ASN ILE PRO TRP SEQRES 19 B 364 ASN GLY GLY LYS MET GLY ASP PRO GLU TYR MET ALA ALA SEQRES 20 B 364 PHE HIS HIS LEU VAL MET PRO ILE ALA ARG GLU PHE ALA SEQRES 21 B 364 PRO GLU LEU VAL LEU VAL SER ALA GLY PHE ASP ALA ALA SEQRES 22 B 364 ARG GLY ASP PRO LEU GLY GLY PHE GLN VAL THR PRO GLU SEQRES 23 B 364 GLY TYR ALA HIS LEU THR HIS GLN LEU MET SER LEU ALA SEQRES 24 B 364 ALA GLY ARG VAL LEU ILE ILE LEU GLU GLY GLY TYR ASN SEQRES 25 B 364 LEU THR SER ILE SER GLU SER MET SER MET CYS THR SER SEQRES 26 B 364 MET LEU LEU GLY ASP SER PRO PRO SER LEU ASP HIS LEU SEQRES 27 B 364 THR PRO LEU LYS THR SER ALA THR VAL SER ILE ASN ASN SEQRES 28 B 364 VAL LEU ARG ALA HIS ALA PRO PHE TRP SER SER LEU ARG HET ZN A2001 1 HET K A2002 1 HET K A2003 1 HET LBH A2004 26 HET GOL A2005 6 HET ZN B2001 1 HET K B2002 1 HET K B2003 1 HET LBH B2004 26 HET GOL B2005 6 HET GOL B2006 6 HET EDO B2007 4 HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM LBH PANOBINOSTAT HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 K 4(K 1+) FORMUL 6 LBH 2(C21 H23 N3 O2) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 14 EDO C2 H6 O2 FORMUL 15 HOH *205(H2 O) HELIX 1 AA1 ASP A 449 LEU A 454 5 6 HELIX 2 AA2 PRO A 467 LEU A 480 1 14 HELIX 3 AA3 LEU A 482 SER A 484 5 3 HELIX 4 AA4 THR A 495 ALA A 500 1 6 HELIX 5 AA5 SER A 504 SER A 514 1 11 HELIX 6 AA6 GLU A 515 MET A 517 5 3 HELIX 7 AA7 LYS A 518 ASP A 527 1 10 HELIX 8 AA8 GLU A 537 THR A 558 1 22 HELIX 9 AA9 ASN A 587 ILE A 599 1 13 HELIX 10 AB1 GLY A 616 PHE A 623 1 8 HELIX 11 AB2 GLU A 638 ALA A 641 5 4 HELIX 12 AB3 SER A 646 ASN A 650 5 5 HELIX 13 AB4 LEU A 656 ARG A 660 5 5 HELIX 14 AB5 GLY A 674 LEU A 685 1 12 HELIX 15 AB6 LEU A 685 ALA A 694 1 10 HELIX 16 AB7 THR A 718 MET A 730 1 13 HELIX 17 AB8 SER A 731 GLY A 735 5 5 HELIX 18 AB9 ASN A 746 LEU A 762 1 17 HELIX 19 AC1 LYS A 776 ALA A 791 1 16 HELIX 20 AC2 TRP A 794 ARG A 798 5 5 HELIX 21 AC3 ASP B 449 LEU B 454 5 6 HELIX 22 AC4 PRO B 467 LEU B 480 1 14 HELIX 23 AC5 LEU B 482 CYS B 486 5 5 HELIX 24 AC6 THR B 495 ALA B 500 1 6 HELIX 25 AC7 SER B 504 SER B 514 1 11 HELIX 26 AC8 GLU B 515 MET B 517 5 3 HELIX 27 AC9 LYS B 518 ASP B 527 1 10 HELIX 28 AD1 GLU B 537 THR B 558 1 22 HELIX 29 AD2 ASN B 587 ILE B 599 1 13 HELIX 30 AD3 GLY B 616 GLU B 624 1 9 HELIX 31 AD4 GLU B 638 ALA B 641 5 4 HELIX 32 AD5 SER B 646 ASN B 650 5 5 HELIX 33 AD6 LEU B 656 ARG B 660 5 5 HELIX 34 AD7 GLY B 674 LEU B 685 1 12 HELIX 35 AD8 LEU B 685 ALA B 694 1 10 HELIX 36 AD9 THR B 718 MET B 730 1 13 HELIX 37 AE1 SER B 731 GLY B 735 5 5 HELIX 38 AE2 ASN B 746 LEU B 762 1 17 HELIX 39 AE3 LYS B 776 ALA B 791 1 16 HELIX 40 AE4 TRP B 794 ARG B 798 5 5 SHEET 1 AA1 8 CYS A 486 ARG A 488 0 SHEET 2 AA1 8 THR A 444 VAL A 447 1 N THR A 444 O HIS A 487 SHEET 3 AA1 8 ASN A 563 ALA A 566 1 O ASN A 563 N GLY A 445 SHEET 4 AA1 8 VAL A 737 LEU A 741 1 O ILE A 739 N ALA A 566 SHEET 5 AA1 8 LEU A 697 ALA A 702 1 N ALA A 702 O ILE A 740 SHEET 6 AA1 8 VAL A 606 ASP A 610 1 N VAL A 609 O LEU A 699 SHEET 7 AA1 8 VAL A 629 ARG A 636 1 O ILE A 632 N ASP A 610 SHEET 8 AA1 8 ASN A 663 TRP A 668 1 O VAL A 664 N TYR A 631 SHEET 1 AA2 8 HIS B 487 ARG B 488 0 SHEET 2 AA2 8 THR B 444 VAL B 447 1 N THR B 444 O HIS B 487 SHEET 3 AA2 8 ASN B 563 ALA B 566 1 O ASN B 563 N GLY B 445 SHEET 4 AA2 8 VAL B 737 LEU B 741 1 O ILE B 739 N ALA B 566 SHEET 5 AA2 8 LEU B 697 ALA B 702 1 N VAL B 698 O LEU B 738 SHEET 6 AA2 8 VAL B 606 ASP B 610 1 N LEU B 607 O LEU B 699 SHEET 7 AA2 8 VAL B 629 ARG B 636 1 O ILE B 632 N ASP B 610 SHEET 8 AA2 8 ASN B 663 TRP B 668 1 O ILE B 666 N SER B 633 LINK O ASP A 610 K K A2002 1555 1555 2.84 LINK OD1 ASP A 610 K K A2002 1555 1555 2.77 LINK OD1 ASP A 612 ZN ZN A2001 1555 1555 2.20 LINK OD2 ASP A 612 ZN ZN A2001 1555 1555 2.70 LINK O ASP A 612 K K A2002 1555 1555 2.65 LINK ND1 HIS A 614 ZN ZN A2001 1555 1555 2.12 LINK O HIS A 614 K K A2002 1555 1555 2.77 LINK O PHE A 623 K K A2003 1555 1555 2.68 LINK O ASP A 626 K K A2003 1555 1555 3.02 LINK O VAL A 629 K K A2003 1555 1555 2.84 LINK OG SER A 633 K K A2002 1555 1555 2.80 LINK O LEU A 634 K K A2002 1555 1555 2.88 LINK O TYR A 662 K K A2003 1555 1555 2.79 LINK OD2 ASP A 705 ZN ZN A2001 1555 1555 2.04 LINK ZN ZN A2001 O2 LBH A2004 1555 1555 2.07 LINK ZN ZN A2001 N3 LBH A2004 1555 1555 2.12 LINK K K A2003 O HOH A2116 1555 1555 3.23 LINK K K A2003 O HOH A2122 1555 1555 2.89 LINK O ASP B 610 K K B2002 1555 1555 2.79 LINK OD1 ASP B 610 K K B2002 1555 1555 2.80 LINK OD1 ASP B 612 ZN ZN B2001 1555 1555 2.09 LINK O ASP B 612 K K B2002 1555 1555 2.69 LINK ND1 HIS B 614 ZN ZN B2001 1555 1555 2.19 LINK O HIS B 614 K K B2002 1555 1555 2.84 LINK O PHE B 623 K K B2003 1555 1555 2.64 LINK O ASP B 626 K K B2003 1555 1555 2.86 LINK O VAL B 629 K K B2003 1555 1555 2.75 LINK OG SER B 633 K K B2002 1555 1555 2.86 LINK O LEU B 634 K K B2002 1555 1555 2.94 LINK O TYR B 662 K K B2003 1555 1555 2.82 LINK OD2 ASP B 705 ZN ZN B2001 1555 1555 1.95 LINK ZN ZN B2001 O1 LBH B2004 1555 1555 2.63 LINK ZN ZN B2001 O2 LBH B2004 1555 1555 2.03 LINK ZN ZN B2001 N3 LBH B2004 1555 1555 2.53 LINK K K B2003 O HOH B2109 1555 1555 2.83 LINK K K B2003 O HOH B2124 1555 1555 3.10 CISPEP 1 ARG A 569 PRO A 570 0 0.16 CISPEP 2 PHE A 643 PRO A 644 0 3.52 CISPEP 3 THR A 773 PRO A 774 0 -0.85 CISPEP 4 ARG B 569 PRO B 570 0 -0.86 CISPEP 5 PHE B 643 PRO B 644 0 4.53 SITE 1 AC1 4 ASP A 612 HIS A 614 ASP A 705 LBH A2004 SITE 1 AC2 5 ASP A 610 ASP A 612 HIS A 614 SER A 633 SITE 2 AC2 5 LEU A 634 SITE 1 AC3 5 PHE A 623 ASP A 626 VAL A 629 TYR A 662 SITE 2 AC3 5 HOH A2122 SITE 1 AC4 14 ASP A 460 HIS A 463 PRO A 464 SER A 531 SITE 2 AC4 14 HIS A 573 HIS A 574 PHE A 583 ASP A 612 SITE 3 AC4 14 HIS A 614 PHE A 643 TYR A 745 LEU A 797 SITE 4 AC4 14 ARG A 798 ZN A2001 SITE 1 AC5 3 ARG A 708 SER A 749 HOH A2112 SITE 1 AC6 4 ASP B 612 HIS B 614 ASP B 705 LBH B2004 SITE 1 AC7 5 ASP B 610 ASP B 612 HIS B 614 SER B 633 SITE 2 AC7 5 LEU B 634 SITE 1 AC8 6 PHE B 623 ASP B 626 VAL B 629 TYR B 662 SITE 2 AC8 6 HOH B2109 HOH B2124 SITE 1 AC9 16 ASP B 460 PRO B 464 SER B 531 HIS B 573 SITE 2 AC9 16 HIS B 574 PHE B 583 ASP B 612 HIS B 614 SITE 3 AC9 16 PHE B 643 ASP B 705 LEU B 712 TYR B 745 SITE 4 AC9 16 LEU B 797 ARG B 798 ZN B2001 GOL B2006 SITE 1 AD1 3 THR B 600 ARG B 601 ARG B 736 SITE 1 AD2 6 PHE B 643 ASN B 645 HIS B 684 PRO B 688 SITE 2 AD2 6 LBH B2004 HOH B2144 SITE 1 AD3 3 ARG B 451 ALA B 491 LEU B 493 CRYST1 65.168 140.396 91.856 90.00 90.00 90.00 P 21 21 2 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 0.015345 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010887 0.00000