HEADER HYDROLASE/HYDROLASE INHIBITOR 23-OCT-15 5EEK TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATALYTIC TITLE 2 DOMAIN 2 IN COMPLEX WITH TRICHOSTATIN A COMPND MOL_ID: 1; COMPND 2 MOLECULE: HDAC6 PROTEIN; COMPND 3 CHAIN: A; 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 4 27-SEP-23 5EEK 1 REMARK LINK REVDAT 3 07-SEP-16 5EEK 1 JRNL REVDAT 2 10-AUG-16 5EEK 1 JRNL REVDAT 1 27-JUL-16 5EEK 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. 1.59 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 55910 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2843 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 44.0274 - 4.3155 1.00 2851 154 0.1559 0.1619 REMARK 3 2 4.3155 - 3.4257 1.00 2724 156 0.1305 0.1627 REMARK 3 3 3.4257 - 2.9928 1.00 2672 169 0.1477 0.1743 REMARK 3 4 2.9928 - 2.7192 1.00 2660 143 0.1413 0.1685 REMARK 3 5 2.7192 - 2.5243 1.00 2654 163 0.1353 0.1530 REMARK 3 6 2.5243 - 2.3755 1.00 2666 147 0.1307 0.1749 REMARK 3 7 2.3755 - 2.2566 1.00 2654 135 0.1192 0.1567 REMARK 3 8 2.2566 - 2.1583 1.00 2638 149 0.1207 0.1548 REMARK 3 9 2.1583 - 2.0752 1.00 2649 137 0.1231 0.1679 REMARK 3 10 2.0752 - 2.0036 1.00 2615 144 0.1144 0.1514 REMARK 3 11 2.0036 - 1.9410 1.00 2674 129 0.1072 0.1472 REMARK 3 12 1.9410 - 1.8855 1.00 2635 124 0.1116 0.1498 REMARK 3 13 1.8855 - 1.8359 1.00 2617 153 0.1109 0.1509 REMARK 3 14 1.8359 - 1.7911 1.00 2606 137 0.1090 0.1525 REMARK 3 15 1.7911 - 1.7504 1.00 2627 139 0.1113 0.1786 REMARK 3 16 1.7504 - 1.7131 1.00 2636 148 0.1136 0.1620 REMARK 3 17 1.7131 - 1.6788 1.00 2624 127 0.1192 0.1668 REMARK 3 18 1.6788 - 1.6472 1.00 2615 122 0.1176 0.1695 REMARK 3 19 1.6472 - 1.6177 1.00 2628 139 0.1221 0.1722 REMARK 3 20 1.6177 - 1.5903 1.00 2622 128 0.1349 0.2064 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.400 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 : 0.009 2948 REMARK 3 ANGLE : 1.296 4005 REMARK 3 CHIRALITY : 0.056 433 REMARK 3 PLANARITY : 0.007 526 REMARK 3 DIHEDRAL : 14.413 1086 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 5EEK 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_1000214789. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28184 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55924 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 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: PDB ENTRY 5EEI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM IODIDE, 20% PEG3350, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K 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 41.94050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.21450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.94050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.21450 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: 6410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 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 I IOD A2007 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 ASP A 770 REMARK 465 HIS A 771 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 SER A 441 OG 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 I IOD A 2026 O HOH A 2234 2.18 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 THR A 600 -88.71 -129.21 REMARK 500 TYR A 637 -51.43 -128.99 REMARK 500 LYS A 672 91.55 58.89 REMARK 500 LEU A 685 -61.90 -123.31 REMARK 500 GLU A 742 -112.95 -111.63 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 71.6 REMARK 620 3 ASP A 612 O 100.1 97.6 REMARK 620 4 HIS A 614 O 165.2 93.9 78.7 REMARK 620 5 SER A 633 OG 85.5 109.5 152.7 102.3 REMARK 620 6 LEU A 634 O 78.2 144.4 69.5 114.5 85.8 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 53.2 REMARK 620 3 HIS A 614 ND1 102.2 155.2 REMARK 620 4 ASP A 705 OD2 106.0 87.9 97.1 REMARK 620 5 TSN A2004 O2 161.2 114.5 90.1 86.2 REMARK 620 6 TSN A2004 O1 87.0 81.9 102.2 153.9 76.5 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 73.4 REMARK 620 3 VAL A 629 O 115.2 73.0 REMARK 620 4 TYR A 662 O 160.2 111.8 84.3 REMARK 620 5 HOH A2131 O 81.5 82.4 143.6 80.4 REMARK 620 6 HOH A2219 O 72.2 144.4 131.0 98.0 84.0 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 TSN A 2004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2010 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2011 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2012 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2013 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2015 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2017 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2018 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2019 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2020 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2022 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2026 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2027 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NH4 A 2028 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 2029 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NH4 A 2030 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NH4 A 2031 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NH4 A 2032 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NH4 A 2033 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NH4 A 2034 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2035 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2036 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 2037 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 2038 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2039 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2040 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues IOD A 2008 and IOD A REMARK 800 2009 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues IOD A 2023 and IOD A REMARK 800 2024 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: 5EEM RELATED DB: PDB REMARK 900 RELATED ID: 5EEN RELATED DB: PDB REMARK 900 RELATED ID: 5EF7 RELATED DB: PDB REMARK 900 RELATED ID: 5EF8 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 5EEK A 440 798 UNP A7YT55 A7YT55_DANRE 288 646 SEQADV 5EEK SER A 435 UNP A7YT55 EXPRESSION TAG SEQADV 5EEK ASN A 436 UNP A7YT55 EXPRESSION TAG SEQADV 5EEK ALA A 437 UNP A7YT55 EXPRESSION TAG SEQADV 5EEK GLY A 438 UNP A7YT55 EXPRESSION TAG SEQADV 5EEK GLY A 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 HET ZN A2001 1 HET K A2002 1 HET K A2003 1 HET TSN A2004 22 HET IOD A2005 1 HET IOD A2006 1 HET IOD A2007 1 HET IOD A2008 2 HET IOD A2009 1 HET IOD A2010 1 HET IOD A2011 2 HET IOD A2012 2 HET IOD A2013 1 HET IOD A2014 1 HET IOD A2015 1 HET IOD A2016 1 HET IOD A2017 1 HET IOD A2018 2 HET IOD A2019 1 HET IOD A2020 1 HET IOD A2021 1 HET IOD A2022 1 HET IOD A2023 1 HET IOD A2024 1 HET IOD A2025 1 HET IOD A2026 2 HET IOD A2027 1 HET NH4 A2028 1 HET CL A2029 1 HET NH4 A2030 1 HET NH4 A2031 1 HET NH4 A2032 1 HET NH4 A2033 1 HET NH4 A2034 1 HET IOD A2035 1 HET IOD A2036 1 HET IOD A2037 1 HET GOL A2038 6 HET EDO A2039 4 HET EDO A2040 4 HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM TSN TRICHOSTATIN A HETNAM IOD IODIDE ION HETNAM NH4 AMMONIUM ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN TSN 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7- HETSYN 2 TSN OXO-2,4-HEPTADIENAMIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 K 2(K 1+) FORMUL 5 TSN C17 H22 N2 O3 FORMUL 6 IOD 26(I 1-) FORMUL 29 NH4 6(H4 N 1+) FORMUL 30 CL CL 1- FORMUL 39 GOL C3 H8 O3 FORMUL 40 EDO 2(C2 H6 O2) FORMUL 42 HOH *376(H2 O) HELIX 1 AA1 ASP A 449 HIS A 455 5 7 HELIX 2 AA2 PRO A 467 LEU A 480 1 14 HELIX 3 AA3 LEU A 482 CYS A 486 5 5 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 GLU A 528 1 11 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 GLU A 624 1 9 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 SHEET 1 AA1 8 HIS A 487 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 VAL A 700 O LEU A 738 SHEET 6 AA1 8 VAL A 606 ASP A 610 1 N LEU A 607 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 LINK O ASP A 610 K K A2002 1555 1555 2.81 LINK OD1 ASP A 610 K K A2002 1555 1555 2.60 LINK OD1 ASP A 612 ZN ZN A2001 1555 1555 1.98 LINK OD2 ASP A 612 ZN ZN A2001 1555 1555 2.69 LINK O ASP A 612 K K A2002 1555 1555 2.54 LINK ND1 HIS A 614 ZN ZN A2001 1555 1555 2.10 LINK O HIS A 614 K K A2002 1555 1555 2.70 LINK O PHE A 623 K K A2003 1555 1555 2.79 LINK O ASP A 626 K K A2003 1555 1555 3.18 LINK O VAL A 629 K K A2003 1555 1555 2.79 LINK OG SER A 633 K K A2002 1555 1555 2.72 LINK O LEU A 634 K K A2002 1555 1555 2.62 LINK O TYR A 662 K K A2003 1555 1555 2.92 LINK OD2 ASP A 705 ZN ZN A2001 1555 1555 1.96 LINK ZN ZN A2001 O2 TSN A2004 1555 1555 2.39 LINK ZN ZN A2001 O1 TSN A2004 1555 1555 2.17 LINK K K A2003 O HOH A2131 1555 1555 2.81 LINK K K A2003 O HOH A2219 1555 1555 2.92 CISPEP 1 ARG A 569 PRO A 570 0 -4.30 CISPEP 2 PHE A 643 PRO A 644 0 7.20 SITE 1 AC1 4 ASP A 612 HIS A 614 ASP A 705 TSN 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 6 PHE A 623 ASP A 626 VAL A 629 TYR A 662 SITE 2 AC3 6 HOH A2131 HOH A2219 SITE 1 AC4 14 HIS A 463 PRO A 464 HIS A 573 HIS A 574 SITE 2 AC4 14 PHE A 583 ASP A 612 HIS A 614 PHE A 643 SITE 3 AC4 14 ASP A 705 LEU A 712 TYR A 745 ZN A2001 SITE 4 AC4 14 GOL A2038 HOH A2309 SITE 1 AC5 2 GLY A 655 NH4 A2031 SITE 1 AC6 4 LYS A 518 PRO A 519 ARG A 520 NH4 A2030 SITE 1 AC7 1 TRP A 459 SITE 1 AC8 1 GLY A 657 SITE 1 AC9 3 HIS A 724 HIS A 727 GLN A 728 SITE 1 AD1 4 ALA A 694 PRO A 695 ALA A 733 NH4 A2032 SITE 1 AD2 1 ARG A 708 SITE 1 AD3 3 PHE A 643 HOH A2198 HOH A2389 SITE 1 AD4 3 SER A 778 HOH A2422 HOH A2424 SITE 1 AD5 2 HIS A 463 HOH A2130 SITE 1 AD6 1 GLN A 450 SITE 1 AD7 6 GLU A 478 ARG A 481 LEU A 483 SER A 484 SITE 2 AD7 6 NH4 A2033 HOH A2435 SITE 1 AD8 3 ARG A 451 NH4 A2028 HOH A2316 SITE 1 AD9 6 SER A 513 ARG A 691 CL A2029 HOH A2234 SITE 2 AD9 6 HOH A2269 HOH A2280 SITE 1 AE1 2 LYS A 776 THR A 777 SITE 1 AE2 2 ARG A 451 IOD A2022 SITE 1 AE3 3 LYS A 512 HIS A 516 IOD A2026 SITE 1 AE4 4 TRP A 459 LYS A 518 IOD A2006 HOH A2184 SITE 1 AE5 5 GLN A 620 HIS A 621 GLU A 624 IOD A2005 SITE 2 AE5 5 HOH A2113 SITE 1 AE6 2 ARG A 691 IOD A2012 SITE 1 AE7 4 ARG A 481 SER A 484 PRO A 792 IOD A2020 SITE 1 AE8 2 ASN A 784 IOD A2035 SITE 1 AE9 1 NH4 A2034 SITE 1 AF1 2 PRO A 774 LEU A 775 SITE 1 AF2 2 HIS A 487 GLN A 560 SITE 1 AF3 6 ARG A 601 ARG A 605 GLU A 696 TSN A2004 SITE 2 AF3 6 HOH A2318 HOH A2327 SITE 1 AF4 3 TYR A 529 SER A 531 HOH A2245 SITE 1 AF5 8 TYR A 448 ASP A 449 GLN A 450 PHE A 474 SITE 2 AF5 8 ARG A 488 HOH A2101 HOH A2106 HOH A2360 SITE 1 AF6 3 SER A 603 PRO A 711 HOH A2433 SITE 1 AF7 3 SER A 505 LYS A 506 HOH A2400 CRYST1 83.881 94.429 51.698 90.00 90.00 90.00 P 21 21 2 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011922 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010590 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019343 0.00000