HEADER HYDROLASE/HYDROLASE INHIBITOR 29-JAN-20 6VNR TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATALYTIC TITLE 2 DOMAIN 2 (CD2) COMPLEXED WITH BISHYDROXAMIC ACID INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HDAC6 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HISTONE DEACETYLASE 6; 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 GENE: HDAC6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE DEACETYLASE, METALLOHYDROLASE, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.D.OSKO,N.J.PORTER,D.W.CHRISTIANSON REVDAT 3 11-OCT-23 6VNR 1 LINK REVDAT 2 15-JUL-20 6VNR 1 JRNL REVDAT 1 13-MAY-20 6VNR 0 JRNL AUTH M.MORGEN,R.R.STEIMBACH,M.GERALDY,L.HELLWEG,P.SEHR, JRNL AUTH 2 J.RIDINGER,O.WITT,I.OEHME,C.J.HERBST-GERVASONI,J.D.OSKO, JRNL AUTH 3 N.J.PORTER,D.W.CHRISTIANSON,N.GUNKEL,A.K.MILLER JRNL TITL DESIGN AND SYNTHESIS OF DIHYDROXAMIC ACIDS AS HDAC6/8/10 JRNL TITL 2 INHIBITORS. JRNL REF CHEMMEDCHEM V. 15 1163 2020 JRNL REFN ESSN 1860-7187 JRNL PMID 32348628 JRNL DOI 10.1002/CMDC.202000149 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.334 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 49180 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.705 REMARK 3 FREE R VALUE TEST SET COUNT : 2314 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 48.3800 - 4.9943 0.84 2687 128 0.1476 0.1626 REMARK 3 2 4.9943 - 3.9647 0.90 2837 125 0.1257 0.1636 REMARK 3 3 3.9647 - 3.4637 0.92 2857 151 0.1355 0.1706 REMARK 3 4 3.4637 - 3.1471 0.80 2517 140 0.1599 0.2181 REMARK 3 5 3.1471 - 2.9215 0.87 2734 115 0.1631 0.2022 REMARK 3 6 2.9215 - 2.7493 0.89 2783 130 0.1623 0.1971 REMARK 3 7 2.7493 - 2.6116 0.91 2821 167 0.1660 0.2157 REMARK 3 8 2.6116 - 2.4980 0.92 2870 138 0.1695 0.2434 REMARK 3 9 2.4980 - 2.4018 0.92 2797 167 0.1682 0.2177 REMARK 3 10 2.4018 - 2.3189 0.81 2552 127 0.1684 0.2049 REMARK 3 11 2.3189 - 2.2464 0.85 2679 136 0.1745 0.2397 REMARK 3 12 2.2464 - 2.1822 0.88 2727 134 0.1700 0.2493 REMARK 3 13 2.1822 - 2.1248 0.89 2748 144 0.1763 0.2491 REMARK 3 14 2.1248 - 2.0729 0.90 2810 110 0.1861 0.2323 REMARK 3 15 2.0729 - 2.0258 0.89 2810 128 0.1906 0.2321 REMARK 3 16 2.0258 - 1.9827 0.91 2861 113 0.1949 0.2541 REMARK 3 17 1.9827 - 1.9430 0.91 2776 161 0.2156 0.2761 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.199 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.974 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.15 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 : 0.006 5681 REMARK 3 ANGLE : 0.818 7719 REMARK 3 CHIRALITY : 0.050 843 REMARK 3 PLANARITY : 0.005 1004 REMARK 3 DIHEDRAL : 10.418 4585 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 6VNR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246706. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-17 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49180 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 48.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 1.700 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.49200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 5EEM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML HDAC6 PROTEIN 2 MM INHIBITOR REMARK 280 0.02 M CITRATE 0.08 M BIS-TRIS PROPANE (PH 8.8) 24% W/V PEG 3350 REMARK 280 1:1 RATIO PROTEIN TO PRECIPITANT, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 53.57000 REMARK 290 SMTRY3 2 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 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 ASP A 770 REMARK 465 HIS A 771 REMARK 465 LEU A 772 REMARK 465 ARG A 798 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 465 LEU B 772 REMARK 465 ARG B 798 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 GLN A 450 OE1 NE2 REMARK 470 GLU A 478 CD OE1 OE2 REMARK 470 GLU A 497 CD OE1 OE2 REMARK 470 ARG A 520 NE CZ NH1 NH2 REMARK 470 GLN A 560 OE1 NE2 REMARK 470 ARG A 562 CZ NH1 NH2 REMARK 470 LYS A 658 CG CD CE NZ REMARK 470 LYS A 672 CE NZ REMARK 470 THR A 773 OG1 CG2 REMARK 470 LYS A 776 CE NZ REMARK 470 GLN B 450 CD OE1 NE2 REMARK 470 LYS B 506 CG CD CE NZ REMARK 470 ARG B 520 CD NE CZ NH1 NH2 REMARK 470 ARG B 524 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 562 CZ NH1 NH2 REMARK 470 LYS B 577 NZ REMARK 470 LYS B 658 CD CE NZ REMARK 470 LYS B 672 CG CD CE NZ 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 O24 R5G A 804 O HOH A 901 2.02 REMARK 500 OE1 GLN A 728 O HOH A 902 2.13 REMARK 500 O ASN A 669 OG SER A 778 2.16 REMARK 500 OH TYR A 745 N02 R5G A 804 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 -92.96 -128.86 REMARK 500 LEU A 685 -63.34 -122.76 REMARK 500 GLN A 716 37.90 -143.65 REMARK 500 GLU A 742 -111.28 -109.77 REMARK 500 SER B 531 60.14 61.33 REMARK 500 CYS B 581 143.83 -175.85 REMARK 500 THR B 600 -93.61 -129.53 REMARK 500 LEU B 685 -60.60 -127.57 REMARK 500 ALA B 702 69.41 -102.49 REMARK 500 GLU B 742 -110.26 -113.44 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 A1125 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A1126 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH B1121 DISTANCE = 5.92 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 A 802 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 O REMARK 620 2 ASP A 610 OD1 70.3 REMARK 620 3 ASP A 612 O 102.4 96.6 REMARK 620 4 HIS A 614 O 165.5 95.3 76.8 REMARK 620 5 SER A 633 OG 84.0 113.0 150.0 104.1 REMARK 620 6 LEU A 634 O 78.9 142.1 68.6 113.6 84.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 612 OD1 REMARK 620 2 HIS A 614 ND1 101.2 REMARK 620 3 ASP A 705 OD2 105.8 94.2 REMARK 620 4 R5G A 804 O01 142.7 114.9 81.4 REMARK 620 5 HOH A 901 O 86.4 98.2 160.6 79.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 803 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 623 O REMARK 620 2 ASP A 626 O 77.2 REMARK 620 3 VAL A 629 O 119.1 82.3 REMARK 620 4 TYR A 662 O 152.2 117.4 87.5 REMARK 620 5 HOH A 942 O 79.5 82.9 152.7 79.2 REMARK 620 6 HOH A1056 O 68.8 144.5 123.2 90.3 81.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 802 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 610 O REMARK 620 2 ASP B 610 OD1 71.1 REMARK 620 3 ASP B 612 O 100.1 96.0 REMARK 620 4 HIS B 614 O 167.4 96.4 79.2 REMARK 620 5 SER B 633 OG 83.4 112.5 150.6 103.5 REMARK 620 6 LEU B 634 O 75.7 139.8 67.9 115.1 85.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 612 OD1 REMARK 620 2 HIS B 614 ND1 105.4 REMARK 620 3 ASP B 705 OD2 105.6 100.1 REMARK 620 4 R5G B 804 N02 163.5 83.0 86.5 REMARK 620 5 R5G B 804 O01 135.6 117.3 79.3 34.4 REMARK 620 6 HOH B 915 O 87.2 90.8 160.0 78.3 80.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 803 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 623 O REMARK 620 2 ASP B 626 O 75.4 REMARK 620 3 VAL B 629 O 118.3 78.0 REMARK 620 4 TYR B 662 O 154.4 118.9 86.6 REMARK 620 5 HOH B 951 O 78.7 88.0 153.4 80.6 REMARK 620 6 HOH B 964 O 70.5 145.5 122.8 91.5 80.9 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 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue R5G A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue R5G B 804 DBREF 6VNR A 440 798 UNP A7YT55 A7YT55_DANRE 288 646 DBREF 6VNR B 440 798 UNP A7YT55 A7YT55_DANRE 288 646 SEQADV 6VNR SER A 435 UNP A7YT55 EXPRESSION TAG SEQADV 6VNR ASN A 436 UNP A7YT55 EXPRESSION TAG SEQADV 6VNR ALA A 437 UNP A7YT55 EXPRESSION TAG SEQADV 6VNR GLY A 438 UNP A7YT55 EXPRESSION TAG SEQADV 6VNR GLY A 439 UNP A7YT55 EXPRESSION TAG SEQADV 6VNR SER B 435 UNP A7YT55 EXPRESSION TAG SEQADV 6VNR ASN B 436 UNP A7YT55 EXPRESSION TAG SEQADV 6VNR ALA B 437 UNP A7YT55 EXPRESSION TAG SEQADV 6VNR GLY B 438 UNP A7YT55 EXPRESSION TAG SEQADV 6VNR 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 A 801 1 HET K A 802 1 HET K A 803 1 HET R5G A 804 24 HET EDO A 805 4 HET EDO A 806 4 HET ZN B 801 1 HET K B 802 1 HET K B 803 1 HET R5G B 804 24 HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM R5G N-HYDROXY-1-{[4-(HYDROXYCARBAMOYL)PHENYL]METHYL}-1H- HETNAM 2 R5G INDOLE-6-CARBOXAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 K 4(K 1+) FORMUL 6 R5G 2(C17 H15 N3 O4) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 13 HOH *447(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 PHE A 623 1 8 HELIX 11 AB2 SER A 646 ASN A 650 5 5 HELIX 12 AB3 LEU A 656 ARG A 660 5 5 HELIX 13 AB4 GLY A 674 LEU A 685 1 12 HELIX 14 AB5 LEU A 685 ALA A 694 1 10 HELIX 15 AB6 THR A 718 MET A 730 1 13 HELIX 16 AB7 SER A 731 GLY A 735 5 5 HELIX 17 AB8 ASN A 746 LEU A 762 1 17 HELIX 18 AB9 LYS A 776 ALA A 791 1 16 HELIX 19 AC1 ASP B 449 LEU B 454 5 6 HELIX 20 AC2 PRO B 467 LEU B 480 1 14 HELIX 21 AC3 LEU B 482 CYS B 486 5 5 HELIX 22 AC4 THR B 495 ALA B 500 1 6 HELIX 23 AC5 SER B 504 SER B 514 1 11 HELIX 24 AC6 GLU B 515 MET B 517 5 3 HELIX 25 AC7 LYS B 518 GLU B 528 1 11 HELIX 26 AC8 GLU B 537 THR B 558 1 22 HELIX 27 AC9 ASN B 587 ILE B 599 1 13 HELIX 28 AD1 GLY B 616 GLU B 624 1 9 HELIX 29 AD2 GLU B 638 ALA B 641 5 4 HELIX 30 AD3 SER B 646 ASN B 650 5 5 HELIX 31 AD4 LEU B 656 ARG B 660 5 5 HELIX 32 AD5 GLY B 674 LEU B 685 1 12 HELIX 33 AD6 LEU B 685 ALA B 694 1 10 HELIX 34 AD7 THR B 718 MET B 730 1 13 HELIX 35 AD8 SER B 731 GLY B 735 5 5 HELIX 36 AD9 ASN B 746 LEU B 762 1 17 HELIX 37 AE1 LYS B 776 ALA B 791 1 16 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 ILE A 740 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 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 ALA B 702 O ILE B 740 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 A 802 1555 1555 2.88 LINK OD1 ASP A 610 K K A 802 1555 1555 2.84 LINK OD1 ASP A 612 ZN ZN A 801 1555 1555 2.03 LINK O ASP A 612 K K A 802 1555 1555 2.55 LINK ND1 HIS A 614 ZN ZN A 801 1555 1555 2.19 LINK O HIS A 614 K K A 802 1555 1555 2.68 LINK O PHE A 623 K K A 803 1555 1555 2.70 LINK O ASP A 626 K K A 803 1555 1555 2.93 LINK O VAL A 629 K K A 803 1555 1555 2.62 LINK OG SER A 633 K K A 802 1555 1555 2.89 LINK O LEU A 634 K K A 802 1555 1555 2.65 LINK O TYR A 662 K K A 803 1555 1555 2.78 LINK OD2 ASP A 705 ZN ZN A 801 1555 1555 1.98 LINK ZN ZN A 801 O01 R5G A 804 1555 1555 2.15 LINK ZN ZN A 801 O HOH A 901 1555 1555 2.20 LINK K K A 803 O HOH A 942 1555 1555 2.73 LINK K K A 803 O HOH A1056 1555 1555 2.99 LINK O ASP B 610 K K B 802 1555 1555 2.88 LINK OD1 ASP B 610 K K B 802 1555 1555 2.77 LINK OD1 ASP B 612 ZN ZN B 801 1555 1555 2.09 LINK O ASP B 612 K K B 802 1555 1555 2.62 LINK ND1 HIS B 614 ZN ZN B 801 1555 1555 2.17 LINK O HIS B 614 K K B 802 1555 1555 2.73 LINK O PHE B 623 K K B 803 1555 1555 2.64 LINK O ASP B 626 K K B 803 1555 1555 2.90 LINK O VAL B 629 K K B 803 1555 1555 2.70 LINK OG SER B 633 K K B 802 1555 1555 2.81 LINK O LEU B 634 K K B 802 1555 1555 2.70 LINK O TYR B 662 K K B 803 1555 1555 2.76 LINK OD2 ASP B 705 ZN ZN B 801 1555 1555 2.09 LINK ZN ZN B 801 N02 R5G B 804 1555 1555 2.42 LINK ZN ZN B 801 O01 R5G B 804 1555 1555 2.03 LINK ZN ZN B 801 O HOH B 915 1555 1555 2.15 LINK K K B 803 O HOH B 951 1555 1555 2.68 LINK K K B 803 O HOH B 964 1555 1555 3.08 CISPEP 1 ARG A 569 PRO A 570 0 -3.28 CISPEP 2 PHE A 643 PRO A 644 0 7.19 CISPEP 3 ARG B 569 PRO B 570 0 -2.86 CISPEP 4 PHE B 643 PRO B 644 0 5.38 SITE 1 AC1 5 ASP A 612 HIS A 614 ASP A 705 R5G A 804 SITE 2 AC1 5 HOH A 901 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 A 942 HOH A1056 SITE 1 AC4 18 SER A 531 HIS A 574 GLY A 582 PHE A 583 SITE 2 AC4 18 ASP A 612 HIS A 614 ALA A 641 PHE A 643 SITE 3 AC4 18 ASN A 645 ASP A 705 GLY A 743 TYR A 745 SITE 4 AC4 18 ZN A 801 HOH A 901 HOH A1057 THR B 777 SITE 5 AC4 18 ASN B 784 ARG B 788 SITE 1 AC5 6 LEU A 557 THR A 600 HOH A 911 HOH A 916 SITE 2 AC5 6 SER B 484 CYS B 486 SITE 1 AC6 6 SER A 484 HOH A 922 HOH A 995 LEU B 557 SITE 2 AC6 6 THR B 600 HOH B 976 SITE 1 AC7 5 ASP B 612 HIS B 614 ASP B 705 R5G B 804 SITE 2 AC7 5 HOH B 915 SITE 1 AC8 5 ASP B 610 ASP B 612 HIS B 614 SER B 633 SITE 2 AC8 5 LEU B 634 SITE 1 AC9 6 PHE B 623 ASP B 626 VAL B 629 TYR B 662 SITE 2 AC9 6 HOH B 951 HOH B 964 SITE 1 AD1 18 VAL A 781 ASN A 784 ARG A 788 SER B 531 SITE 2 AD1 18 HIS B 574 GLY B 582 PHE B 583 ASP B 612 SITE 3 AD1 18 HIS B 614 ALA B 641 PHE B 643 ASN B 645 SITE 4 AD1 18 ASP B 705 GLY B 743 TYR B 745 ZN B 801 SITE 5 AD1 18 HOH B 915 HOH B1065 CRYST1 48.380 107.140 74.350 90.00 90.00 90.00 P 1 21 1 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 0.020670 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009334 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013450 0.00000