HEADER HYDROLASE 29-JUL-19 6PYE TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATALYTIC TITLE 2 DOMAIN 2 COMPLEXED WITH NR160 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 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 EXPDTA X-RAY DIFFRACTION AUTHOR J.D.OSKO,D.W.CHRISTIANSON REVDAT 4 11-OCT-23 6PYE 1 REMARK REVDAT 3 07-OCT-20 6PYE 1 JRNL REVDAT 2 30-SEP-20 6PYE 1 JRNL REVDAT 1 29-JUL-20 6PYE 0 JRNL AUTH N.RESSING,M.SONNICHSEN,J.D.OSKO,A.SCHOLER,J.SCHLIEHE-DIECKS, JRNL AUTH 2 A.SKERHUT,A.BORKHARDT,J.HAUER,M.U.KASSACK,D.W.CHRISTIANSON, JRNL AUTH 3 S.BHATIA,F.K.HANSEN JRNL TITL MULTICOMPONENT SYNTHESIS, BINDING MODE, AND JRNL TITL 2 STRUCTURE-ACTIVITY RELATIONSHIP OF SELECTIVE HISTONE JRNL TITL 3 DEACETYLASE 6 (HDAC6) INHIBITORS WITH BIFURCATED CAPPING JRNL TITL 4 GROUPS. JRNL REF J.MED.CHEM. V. 63 10339 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32803970 JRNL DOI 10.1021/ACS.JMEDCHEM.9B01888 REMARK 2 REMARK 2 RESOLUTION. 1.48 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.336 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 127210 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) : 0.164 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.972 REMARK 3 FREE R VALUE TEST SET COUNT : 6325 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 60.3180 - 4.5981 0.97 4157 201 0.1375 0.1363 REMARK 3 2 4.5981 - 3.6497 0.96 4032 194 0.1258 0.1398 REMARK 3 3 3.6497 - 3.1884 0.97 4061 217 0.1470 0.1686 REMARK 3 4 3.1884 - 2.8969 0.98 4096 211 0.1584 0.1619 REMARK 3 5 2.8969 - 2.6893 0.99 4139 209 0.1580 0.1646 REMARK 3 6 2.6893 - 2.5307 0.93 3891 195 0.1581 0.1852 REMARK 3 7 2.5307 - 2.4040 0.97 4098 181 0.1617 0.1543 REMARK 3 8 2.4040 - 2.2993 0.97 4003 234 0.1612 0.1868 REMARK 3 9 2.2993 - 2.2108 0.98 4028 215 0.1588 0.1880 REMARK 3 10 2.2108 - 2.1345 0.98 4096 228 0.1663 0.1584 REMARK 3 11 2.1345 - 2.0678 0.98 4060 224 0.1709 0.2093 REMARK 3 12 2.0678 - 2.0087 0.93 3870 194 0.1713 0.1923 REMARK 3 13 2.0087 - 1.9558 0.96 3997 196 0.1707 0.1951 REMARK 3 14 1.9558 - 1.9081 0.98 4050 221 0.1720 0.2001 REMARK 3 15 1.9081 - 1.8647 0.98 4052 222 0.1746 0.2060 REMARK 3 16 1.8647 - 1.8250 0.97 4027 213 0.1784 0.2303 REMARK 3 17 1.8250 - 1.7885 0.98 4058 243 0.1800 0.1993 REMARK 3 18 1.7885 - 1.7547 0.98 4064 207 0.1840 0.1975 REMARK 3 19 1.7547 - 1.7234 0.98 4050 205 0.1846 0.2178 REMARK 3 20 1.7234 - 1.6942 0.94 3909 231 0.1901 0.2038 REMARK 3 21 1.6942 - 1.6668 0.95 3908 173 0.1878 0.1979 REMARK 3 22 1.6668 - 1.6412 0.97 4068 199 0.1894 0.2107 REMARK 3 23 1.6412 - 1.6171 0.98 4039 203 0.1890 0.2057 REMARK 3 24 1.6171 - 1.5943 0.98 4071 214 0.1901 0.2123 REMARK 3 25 1.5943 - 1.5727 0.98 4014 222 0.1889 0.2207 REMARK 3 26 1.5727 - 1.5523 0.98 4043 225 0.2011 0.2121 REMARK 3 27 1.5523 - 1.5329 0.98 4009 200 0.2059 0.2509 REMARK 3 28 1.5329 - 1.5144 0.98 4041 253 0.2133 0.2393 REMARK 3 29 1.5144 - 1.4968 0.98 4043 204 0.2148 0.2245 REMARK 3 30 1.4968 - 1.4800 0.95 3911 191 0.2325 0.2654 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) : 0.128 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.067 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.15 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 5906 REMARK 3 ANGLE : 0.840 8058 REMARK 3 CHIRALITY : 0.080 878 REMARK 3 PLANARITY : 0.006 1055 REMARK 3 DIHEDRAL : 10.021 4595 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 6PYE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000243252. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-19 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-C 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 : CRYO-COOLED DOUBLE CRYSTAL REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 127210 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 60.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 5EEM REMARK 200 REMARK 200 REMARK: PLATE-LIKE CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML ZCD2 PROTEIN, 2 MM NR160 REMARK 280 INHIBITOR, 0.2 M AMMONIUM CITRATE TRIBASIC, PH 7.0, 20% W/V REMARK 280 PEG3350, 1:1 RATIO PROTEIN TO PRECIPITANT, VAPOR DIFFUSION, REMARK 280 SITTING DROP, 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 41.56500 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 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 GLN A 450 CD OE1 NE2 REMARK 470 GLU A 497 CD OE1 OE2 REMARK 470 LYS A 506 CD CE NZ REMARK 470 LYS A 518 CD CE NZ REMARK 470 ARG A 520 CD NE CZ NH1 NH2 REMARK 470 LYS A 672 CD CE NZ REMARK 470 HIS B 462 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 506 CD CE NZ REMARK 470 ARG B 520 CZ NH1 NH2 REMARK 470 ARG B 524 CD NE CZ NH1 NH2 REMARK 470 ARG B 562 NE CZ NH1 NH2 REMARK 470 LYS B 658 CD CE NZ REMARK 470 LYS B 672 CG CD CE NZ REMARK 470 ASP B 770 CG OD1 OD2 REMARK 470 HIS B 771 CG ND1 CD2 CE1 NE2 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 O HOH A 912 O HOH A 1300 2.12 REMARK 500 O HOH A 907 O HOH A 1247 2.13 REMARK 500 O HOH A 1252 O HOH A 1346 2.17 REMARK 500 O HOH A 1266 O HOH A 1284 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 -53.02 -123.27 REMARK 500 THR A 600 -51.12 -124.39 REMARK 500 ARG A 601 131.58 -170.29 REMARK 500 LEU A 685 -60.56 -127.53 REMARK 500 GLN A 716 40.40 -140.62 REMARK 500 GLU A 742 -111.38 -110.21 REMARK 500 THR B 600 -53.22 -126.38 REMARK 500 THR B 600 -54.33 -125.67 REMARK 500 ARG B 601 132.64 -170.63 REMARK 500 LEU B 685 -59.97 -127.89 REMARK 500 GLN B 716 37.94 -140.31 REMARK 500 GLU B 742 -111.76 -109.54 REMARK 500 HIS B 771 -85.91 52.08 REMARK 500 LEU B 772 102.21 90.78 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 A1355 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A1356 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A1357 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A1358 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A1359 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH A1360 DISTANCE = 7.11 ANGSTROMS REMARK 525 HOH B1250 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH B1251 DISTANCE = 6.40 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 805 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 O REMARK 620 2 ASP A 610 OD1 70.6 REMARK 620 3 ASP A 612 O 99.8 96.9 REMARK 620 4 HIS A 614 O 164.3 94.0 78.7 REMARK 620 5 SER A 633 OG 84.8 111.3 151.3 104.1 REMARK 620 6 LEU A 634 O 77.6 141.6 67.6 115.4 86.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 804 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 612 OD2 REMARK 620 2 HIS A 614 ND1 100.2 REMARK 620 3 ASP A 705 OD2 105.6 97.3 REMARK 620 4 P5Y A 801 O01 169.8 80.4 84.4 REMARK 620 5 P5Y A 801 O37 96.0 102.8 147.3 74.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 806 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 623 O REMARK 620 2 ASP A 626 O 75.3 REMARK 620 3 VAL A 629 O 117.6 76.3 REMARK 620 4 TYR A 662 O 155.1 117.9 87.0 REMARK 620 5 HOH A1027 O 70.1 145.0 124.9 92.7 REMARK 620 6 HOH A1057 O 80.4 89.4 152.2 78.8 79.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 808 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 610 O REMARK 620 2 ASP B 610 OD1 70.6 REMARK 620 3 ASP B 612 O 98.9 98.3 REMARK 620 4 HIS B 614 O 164.1 93.7 80.5 REMARK 620 5 SER B 633 OG 84.0 109.6 151.2 104.3 REMARK 620 6 LEU B 634 O 76.5 141.2 66.9 117.1 86.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 807 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 612 OD1 REMARK 620 2 HIS B 614 ND1 100.2 REMARK 620 3 ASP B 705 OD2 103.9 99.0 REMARK 620 4 P5Y B 801 N36 119.6 82.1 135.6 REMARK 620 5 P5Y B 801 O01 172.6 82.0 82.6 53.5 REMARK 620 6 P5Y B 801 O37 96.0 105.4 145.1 30.4 76.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 809 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 623 O REMARK 620 2 ASP B 626 O 75.1 REMARK 620 3 VAL B 629 O 117.7 77.5 REMARK 620 4 TYR B 662 O 155.3 117.4 86.6 REMARK 620 5 HOH B1009 O 79.2 86.1 151.7 80.5 REMARK 620 6 HOH B1012 O 69.5 144.0 124.9 93.6 81.2 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 P5Y A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P5Y B 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 807 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 808 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 809 DBREF 6PYE A 440 798 UNP A7YT55 A7YT55_DANRE 288 646 DBREF 6PYE B 440 798 UNP A7YT55 A7YT55_DANRE 288 646 SEQADV 6PYE SER A 435 UNP A7YT55 EXPRESSION TAG SEQADV 6PYE ASN A 436 UNP A7YT55 EXPRESSION TAG SEQADV 6PYE ALA A 437 UNP A7YT55 EXPRESSION TAG SEQADV 6PYE GLY A 438 UNP A7YT55 EXPRESSION TAG SEQADV 6PYE GLY A 439 UNP A7YT55 EXPRESSION TAG SEQADV 6PYE SER B 435 UNP A7YT55 EXPRESSION TAG SEQADV 6PYE ASN B 436 UNP A7YT55 EXPRESSION TAG SEQADV 6PYE ALA B 437 UNP A7YT55 EXPRESSION TAG SEQADV 6PYE GLY B 438 UNP A7YT55 EXPRESSION TAG SEQADV 6PYE 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 P5Y A 801 37 HET EDO A 802 4 HET EDO A 803 4 HET ZN A 804 1 HET K A 805 1 HET K A 806 1 HET P5Y B 801 37 HET EDO B 802 4 HET EDO B 803 4 HET EDO B 804 4 HET EDO B 805 4 HET EDO B 806 4 HET ZN B 807 1 HET K B 808 1 HET K B 809 1 HETNAM P5Y N-[(1-BENZYL-1H-TETRAZOL-5-YL)METHYL]-N-{[4- HETNAM 2 P5Y (HYDROXYCARBAMOYL)PHENYL]METHYL}-2-(TRIFLUOROMETHYL) HETNAM 3 P5Y BENZAMIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 P5Y 2(C25 H21 F3 N6 O3) FORMUL 4 EDO 7(C2 H6 O2) FORMUL 6 ZN 2(ZN 2+) FORMUL 7 K 4(K 1+) FORMUL 18 HOH *810(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 THR A 600 1 14 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 HIS B 455 5 7 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 GLU B 528 1 11 HELIX 28 AD1 GLU B 537 THR B 558 1 22 HELIX 29 AD2 ASN B 587 THR B 600 1 14 HELIX 30 AD3 GLY B 616 PHE B 623 1 8 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 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 VAL B 700 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 VAL B 664 N TYR B 631 LINK O ASP A 610 K K A 805 1555 1555 2.82 LINK OD1 ASP A 610 K K A 805 1555 1555 2.77 LINK OD2 ASP A 612 ZN ZN A 804 1555 1555 2.00 LINK O ASP A 612 K K A 805 1555 1555 2.61 LINK ND1 HIS A 614 ZN ZN A 804 1555 1555 2.11 LINK O HIS A 614 K K A 805 1555 1555 2.69 LINK O PHE A 623 K K A 806 1555 1555 2.73 LINK O ASP A 626 K K A 806 1555 1555 2.94 LINK O VAL A 629 K K A 806 1555 1555 2.67 LINK OG SER A 633 K K A 805 1555 1555 2.75 LINK O LEU A 634 K K A 805 1555 1555 2.70 LINK O TYR A 662 K K A 806 1555 1555 2.79 LINK OD2 ASP A 705 ZN ZN A 804 1555 1555 1.97 LINK O01 P5Y A 801 ZN ZN A 804 1555 1555 2.50 LINK O37 P5Y A 801 ZN ZN A 804 1555 1555 2.00 LINK K K A 806 O HOH A1027 1555 1555 2.97 LINK K K A 806 O HOH A1057 1555 1555 2.75 LINK O ASP B 610 K K B 808 1555 1555 2.81 LINK OD1 ASP B 610 K K B 808 1555 1555 2.72 LINK OD1 ASP B 612 ZN ZN B 807 1555 1555 2.00 LINK O ASP B 612 K K B 808 1555 1555 2.60 LINK ND1 HIS B 614 ZN ZN B 807 1555 1555 2.11 LINK O HIS B 614 K K B 808 1555 1555 2.71 LINK O PHE B 623 K K B 809 1555 1555 2.73 LINK O ASP B 626 K K B 809 1555 1555 2.93 LINK O VAL B 629 K K B 809 1555 1555 2.66 LINK OG SER B 633 K K B 808 1555 1555 2.73 LINK O LEU B 634 K K B 808 1555 1555 2.73 LINK O TYR B 662 K K B 809 1555 1555 2.79 LINK OD2 ASP B 705 ZN ZN B 807 1555 1555 1.99 LINK N36 P5Y B 801 ZN ZN B 807 1555 1555 2.58 LINK O01 P5Y B 801 ZN ZN B 807 1555 1555 2.45 LINK O37 P5Y B 801 ZN ZN B 807 1555 1555 1.85 LINK K K B 809 O HOH B1009 1555 1555 2.70 LINK K K B 809 O HOH B1012 1555 1555 3.00 CISPEP 1 ARG A 569 PRO A 570 0 -2.49 CISPEP 2 PHE A 643 PRO A 644 0 7.51 CISPEP 3 ARG B 569 PRO B 570 0 -2.27 CISPEP 4 PHE B 643 PRO B 644 0 6.98 SITE 1 AC1 16 HIS A 463 SER A 531 HIS A 573 HIS A 574 SITE 2 AC1 16 GLY A 582 PHE A 583 ASP A 612 HIS A 614 SITE 3 AC1 16 PHE A 643 ASN A 645 ASP A 705 LEU A 712 SITE 4 AC1 16 TYR A 745 ZN A 804 HOH A 963 HOH A1072 SITE 1 AC2 8 GLN A 468 SER A 471 ARG A 472 SER A 475 SITE 2 AC2 8 HOH A 908 HOH A1106 HOH A1131 HOH A1217 SITE 1 AC3 3 PHE A 474 ARG A 488 HOH A1134 SITE 1 AC4 4 ASP A 612 HIS A 614 ASP A 705 P5Y A 801 SITE 1 AC5 5 ASP A 610 ASP A 612 HIS A 614 SER A 633 SITE 2 AC5 5 LEU A 634 SITE 1 AC6 6 PHE A 623 ASP A 626 VAL A 629 TYR A 662 SITE 2 AC6 6 HOH A1027 HOH A1057 SITE 1 AC7 17 HIS B 463 PRO B 464 SER B 531 HIS B 573 SITE 2 AC7 17 HIS B 574 GLY B 582 PHE B 583 ASP B 612 SITE 3 AC7 17 HIS B 614 PHE B 643 ASN B 645 ASP B 705 SITE 4 AC7 17 LEU B 712 TYR B 745 ZN B 807 HOH B1018 SITE 5 AC7 17 HOH B1035 SITE 1 AC8 7 SER B 471 ARG B 472 SER B 475 HOH B 921 SITE 2 AC8 7 HOH B1014 HOH B1049 HOH B1184 SITE 1 AC9 4 ARG A 476 GLU A 479 ASN B 746 SER B 749 SITE 1 AD1 4 PHE B 474 ARG B 488 HOH B 931 HOH B1136 SITE 1 AD2 7 ALA B 707 GLY B 709 ASP B 710 GLY B 714 SITE 2 AD2 7 PHE B 715 HOH B 901 HOH B 987 SITE 1 AD3 4 SER B 475 GLU B 478 GLU B 479 HOH B1137 SITE 1 AD4 4 ASP B 612 HIS B 614 ASP B 705 P5Y B 801 SITE 1 AD5 5 ASP B 610 ASP B 612 HIS B 614 SER B 633 SITE 2 AD5 5 LEU B 634 SITE 1 AD6 6 PHE B 623 ASP B 626 VAL B 629 TYR B 662 SITE 2 AD6 6 HOH B1009 HOH B1012 CRYST1 55.000 83.130 88.590 90.00 98.33 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 0.018182 0.000000 0.002662 0.00000 SCALE2 0.000000 0.012029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011408 0.00000