HEADER HYDROLASE/HYDROLASE INHIBITOR 27-JAN-14 4OVZ TITLE X-RAY STRUCTURAL AND BIOLOGICAL EVALUATION OF A SERIES OF POTENT AND TITLE 2 HIGHLY SELECTIVE INHIBITORS OF HUMAN CORONAVIRUS PAPAIN-LIKE TITLE 3 PROTEASES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN-LIKE PROTEINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NON-STRUCTURAL PROTEIN 3, NSP3, PL2-PRO, PL-PRO, SARS COMPND 5 CORONAVIRUS MAIN PROTEINASE; COMPND 6 EC: 3.4.19.12,3.4.22.69; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PAPAIN-LIKE PROTEINASE; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: NON-STRUCTURAL PROTEIN 3, NSP3, PL2-PRO, PL-PRO, SARS COMPND 12 CORONAVIRUS MAIN PROTEINASE; COMPND 13 EC: 3.4.19.12,3.4.22.69; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS; SOURCE 3 ORGANISM_TAXID: 228330; SOURCE 4 STRAIN: URBANI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS; SOURCE 11 ORGANISM_TAXID: 228330; SOURCE 12 STRAIN: URBANI; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS COV, CORONAVIRUS, HCOV, HUMAN CORONAVIRUS, SARS, SEVERE ACUTE KEYWDS 2 RESPIRATORY SYNDROME, MERS, MIDDLE EAST RESPIRATORY SYNDROME, PLPRO, KEYWDS 3 PROTEASE INHIBITOR, COMPLEX, DUB, DEUBIQUITINATING ENZYME, KEYWDS 4 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.M.BAEZ-SANTOS,A.MESECAR REVDAT 5 15-NOV-23 4OVZ 1 REMARK REVDAT 4 27-SEP-23 4OVZ 1 REMARK REVDAT 3 22-NOV-17 4OVZ 1 SOURCE REMARK REVDAT 2 30-APR-14 4OVZ 1 SEQADV SEQRES REVDAT 1 23-APR-14 4OVZ 0 JRNL AUTH Y.M.BAEZ-SANTOS,S.J.BARRAZA,M.W.WILSON,M.P.AGIUS, JRNL AUTH 2 A.M.MIELECH,N.M.DAVIS,S.C.BAKER,S.D.LARSEN,A.D.MESECAR JRNL TITL X-RAY STRUCTURAL AND BIOLOGICAL EVALUATION OF A SERIES OF JRNL TITL 2 POTENT AND HIGHLY SELECTIVE INHIBITORS OF HUMAN CORONAVIRUS JRNL TITL 3 PAPAIN-LIKE PROTEASES. JRNL REF J.MED.CHEM. V. 57 2393 2014 JRNL REFN ISSN 1520-4804 JRNL PMID 24568342 JRNL DOI 10.1021/JM401712T REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.8 REMARK 3 NUMBER OF REFLECTIONS : 24909 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1265 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 35.7499 - 5.1877 0.99 3116 179 0.2253 0.2966 REMARK 3 2 5.1877 - 4.1196 1.00 3055 167 0.1719 0.2404 REMARK 3 3 4.1196 - 3.5994 1.00 3061 175 0.1640 0.2051 REMARK 3 4 3.5994 - 3.2705 1.00 3074 146 0.1676 0.2054 REMARK 3 5 3.2705 - 3.0362 1.00 3055 155 0.1784 0.2274 REMARK 3 6 3.0362 - 2.8573 1.00 3036 157 0.1851 0.2656 REMARK 3 7 2.8573 - 2.7143 0.92 2762 155 0.1835 0.2688 REMARK 3 8 2.7143 - 2.5962 0.53 1619 81 0.1688 0.2596 REMARK 3 9 2.5962 - 2.5000 0.29 866 50 0.1623 0.2354 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.65 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 : 0.026 4580 REMARK 3 ANGLE : 1.735 6209 REMARK 3 CHIRALITY : 0.124 686 REMARK 3 PLANARITY : 0.008 779 REMARK 3 DIHEDRAL : 18.581 1631 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 4OVZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000200072. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24909 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.69600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3MJ5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CITRATE, PH 5.5, 40% REMARK 280 (V/V) PEG 600, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 59.88600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.75400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.88600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.75400 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 VAL A 3 REMARK 465 LYS A 4 REMARK 465 THR A 5 REMARK 465 ILE A 6 REMARK 465 LYS A 7 REMARK 465 VAL A 8 REMARK 465 THR A 314 REMARK 465 ILE A 315 REMARK 465 LYS A 316 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 VAL B 3 REMARK 465 LYS B 4 REMARK 465 THR B 5 REMARK 465 ILE B 6 REMARK 465 LYS B 7 REMARK 465 VAL B 8 REMARK 465 PHE B 9 REMARK 465 THR B 10 REMARK 465 THR B 11 REMARK 465 VAL B 12 REMARK 465 ASP B 13 REMARK 465 ASN B 14 REMARK 465 THR B 15 REMARK 465 ASN B 16 REMARK 465 LEU B 17 REMARK 465 HIS B 18 REMARK 465 THR B 19 REMARK 465 GLN B 20 REMARK 465 LEU B 21 REMARK 465 VAL B 22 REMARK 465 ASP B 23 REMARK 465 MET B 24 REMARK 465 SER B 25 REMARK 465 MET B 26 REMARK 465 THR B 27 REMARK 465 TYR B 28 REMARK 465 GLY B 29 REMARK 465 GLN B 30 REMARK 465 GLN B 31 REMARK 465 PHE B 32 REMARK 465 GLY B 33 REMARK 465 PRO B 34 REMARK 465 THR B 35 REMARK 465 TYR B 36 REMARK 465 LEU B 37 REMARK 465 ASP B 38 REMARK 465 GLY B 39 REMARK 465 ALA B 40 REMARK 465 ASP B 41 REMARK 465 VAL B 42 REMARK 465 THR B 43 REMARK 465 LYS B 44 REMARK 465 ILE B 45 REMARK 465 LYS B 46 REMARK 465 PRO B 47 REMARK 465 HIS B 48 REMARK 465 VAL B 49 REMARK 465 ASN B 50 REMARK 465 HIS B 51 REMARK 465 GLU B 52 REMARK 465 GLY B 53 REMARK 465 LYS B 54 REMARK 465 THR B 55 REMARK 465 PHE B 56 REMARK 465 PHE B 57 REMARK 465 VAL B 58 REMARK 465 LEU B 59 REMARK 465 PRO B 60 REMARK 465 SER B 61 REMARK 465 ASP B 62 REMARK 465 ASP B 63 REMARK 465 THR B 64 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 OE2 GLU A 281 OH TYR A 284 1.74 REMARK 500 OH TYR B 84 OD1 ASN B 147 2.13 REMARK 500 O ALA A 231 O HOH A 1023 2.17 REMARK 500 O HOH B 1001 O HOH B 1003 2.18 REMARK 500 O LEU A 59 N SER A 61 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 45 CG1 - CB - CG2 ANGL. DEV. = 14.0 DEGREES REMARK 500 ASP A 77 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 184 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES 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 19 126.47 -31.96 REMARK 500 SER A 25 -79.99 -44.03 REMARK 500 LEU A 37 120.17 175.07 REMARK 500 ASP A 38 53.56 39.65 REMARK 500 ALA A 40 83.90 -44.79 REMARK 500 ASP A 41 120.45 -37.73 REMARK 500 PRO A 47 155.45 -48.53 REMARK 500 ASN A 50 -65.95 -125.18 REMARK 500 PRO A 60 70.67 -44.05 REMARK 500 ASP A 63 -19.98 -45.80 REMARK 500 OCS A 112 -74.23 5.49 REMARK 500 HIS A 192 58.55 -118.32 REMARK 500 CYS A 193 -169.39 175.18 REMARK 500 CYS A 227 -14.19 -165.92 REMARK 500 ASP A 230 147.13 -30.37 REMARK 500 LEU A 260 -60.53 -100.27 REMARK 500 LYS A 280 -126.56 -105.00 REMARK 500 THR A 309 -62.14 -138.30 REMARK 500 SER B 104 -169.78 -110.93 REMARK 500 LYS B 196 131.81 158.16 REMARK 500 PRO B 224 63.23 -67.14 REMARK 500 CYS B 225 174.56 -57.53 REMARK 500 ARG B 229 -114.30 -116.85 REMARK 500 ALA B 231 114.60 168.37 REMARK 500 LYS B 280 -118.89 -126.39 REMARK 500 THR B 309 -55.16 -137.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 111 OCS A 112 147.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 1030 REMARK 615 HOH A 1033 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 ZN A 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 190 SG REMARK 620 2 CYS A 193 SG 97.2 REMARK 620 3 CYS A 225 SG 89.8 168.0 REMARK 620 4 CYS A 227 SG 169.9 91.4 82.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 190 SG REMARK 620 2 CYS B 193 SG 86.2 REMARK 620 3 CYS B 227 SG 143.7 107.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 903 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 218 O REMARK 620 2 LEU B 235 O 118.3 REMARK 620 3 TYR B 311 OH 123.1 106.9 REMARK 620 4 THR B 313 OG1 128.2 84.2 87.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P85 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P85 B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 907 DBREF 4OVZ A 2 316 UNP P0C6U8 R1A_CVHSA 1541 1855 DBREF 4OVZ B 2 316 UNP P0C6U8 R1A_CVHSA 1541 1855 SEQADV 4OVZ MET A 1 UNP P0C6U8 INITIATING METHIONINE SEQADV 4OVZ MET B 1 UNP P0C6U8 INITIATING METHIONINE SEQRES 1 A 316 MET GLU VAL LYS THR ILE LYS VAL PHE THR THR VAL ASP SEQRES 2 A 316 ASN THR ASN LEU HIS THR GLN LEU VAL ASP MET SER MET SEQRES 3 A 316 THR TYR GLY GLN GLN PHE GLY PRO THR TYR LEU ASP GLY SEQRES 4 A 316 ALA ASP VAL THR LYS ILE LYS PRO HIS VAL ASN HIS GLU SEQRES 5 A 316 GLY LYS THR PHE PHE VAL LEU PRO SER ASP ASP THR LEU SEQRES 6 A 316 ARG SER GLU ALA PHE GLU TYR TYR HIS THR LEU ASP GLU SEQRES 7 A 316 SER PHE LEU GLY ARG TYR MET SER ALA LEU ASN HIS THR SEQRES 8 A 316 LYS LYS TRP LYS PHE PRO GLN VAL GLY GLY LEU THR SER SEQRES 9 A 316 ILE LYS TRP ALA ASP ASN ASN OCS TYR LEU SER SER VAL SEQRES 10 A 316 LEU LEU ALA LEU GLN GLN LEU GLU VAL LYS PHE ASN ALA SEQRES 11 A 316 PRO ALA LEU GLN GLU ALA TYR TYR ARG ALA ARG ALA GLY SEQRES 12 A 316 ASP ALA ALA ASN PHE CYS ALA LEU ILE LEU ALA TYR SER SEQRES 13 A 316 ASN LYS THR VAL GLY GLU LEU GLY ASP VAL ARG GLU THR SEQRES 14 A 316 MET THR HIS LEU LEU GLN HIS ALA ASN LEU GLU SER ALA SEQRES 15 A 316 LYS ARG VAL LEU ASN VAL VAL CYS LYS HIS CYS GLY GLN SEQRES 16 A 316 LYS THR THR THR LEU THR GLY VAL GLU ALA VAL MET TYR SEQRES 17 A 316 MET GLY THR LEU SER TYR ASP ASN LEU LYS THR GLY VAL SEQRES 18 A 316 SER ILE PRO CYS VAL CYS GLY ARG ASP ALA THR GLN TYR SEQRES 19 A 316 LEU VAL GLN GLN GLU SER SER PHE VAL MET MET SER ALA SEQRES 20 A 316 PRO PRO ALA GLU TYR LYS LEU GLN GLN GLY THR PHE LEU SEQRES 21 A 316 CYS ALA ASN GLU TYR THR GLY ASN TYR GLN CSO GLY HIS SEQRES 22 A 316 TYR THR HIS ILE THR ALA LYS GLU THR LEU TYR ARG ILE SEQRES 23 A 316 ASP GLY ALA HIS LEU THR LYS MET SER GLU TYR LYS GLY SEQRES 24 A 316 PRO VAL THR ASP VAL PHE TYR LYS GLU THR SER TYR THR SEQRES 25 A 316 THR THR ILE LYS SEQRES 1 B 316 MET GLU VAL LYS THR ILE LYS VAL PHE THR THR VAL ASP SEQRES 2 B 316 ASN THR ASN LEU HIS THR GLN LEU VAL ASP MET SER MET SEQRES 3 B 316 THR TYR GLY GLN GLN PHE GLY PRO THR TYR LEU ASP GLY SEQRES 4 B 316 ALA ASP VAL THR LYS ILE LYS PRO HIS VAL ASN HIS GLU SEQRES 5 B 316 GLY LYS THR PHE PHE VAL LEU PRO SER ASP ASP THR LEU SEQRES 6 B 316 ARG SER GLU ALA PHE GLU TYR TYR HIS THR LEU ASP GLU SEQRES 7 B 316 SER PHE LEU GLY ARG TYR MET SER ALA LEU ASN HIS THR SEQRES 8 B 316 LYS LYS TRP LYS PHE PRO GLN VAL GLY GLY LEU THR SER SEQRES 9 B 316 ILE LYS TRP ALA ASP ASN ASN OCS TYR LEU SER SER VAL SEQRES 10 B 316 LEU LEU ALA LEU GLN GLN LEU GLU VAL LYS PHE ASN ALA SEQRES 11 B 316 PRO ALA LEU GLN GLU ALA TYR TYR ARG ALA ARG ALA GLY SEQRES 12 B 316 ASP ALA ALA ASN PHE CYS ALA LEU ILE LEU ALA TYR SER SEQRES 13 B 316 ASN LYS THR VAL GLY GLU LEU GLY ASP VAL ARG GLU THR SEQRES 14 B 316 MET THR HIS LEU LEU GLN HIS ALA ASN LEU GLU SER ALA SEQRES 15 B 316 LYS ARG VAL LEU ASN VAL VAL CYS LYS HIS CYS GLY GLN SEQRES 16 B 316 LYS THR THR THR LEU THR GLY VAL GLU ALA VAL MET TYR SEQRES 17 B 316 MET GLY THR LEU SER TYR ASP ASN LEU LYS THR GLY VAL SEQRES 18 B 316 SER ILE PRO CYS VAL CYS GLY ARG ASP ALA THR GLN TYR SEQRES 19 B 316 LEU VAL GLN GLN GLU SER SER PHE VAL MET MET SER ALA SEQRES 20 B 316 PRO PRO ALA GLU TYR LYS LEU GLN GLN GLY THR PHE LEU SEQRES 21 B 316 CYS ALA ASN GLU TYR THR GLY ASN TYR GLN CYS GLY HIS SEQRES 22 B 316 TYR THR HIS ILE THR ALA LYS GLU THR LEU TYR ARG ILE SEQRES 23 B 316 ASP GLY ALA HIS LEU THR LYS MET SER GLU TYR LYS GLY SEQRES 24 B 316 PRO VAL THR ASP VAL PHE TYR LYS GLU THR SER TYR THR SEQRES 25 B 316 THR THR ILE LYS MODRES 4OVZ OCS A 112 CYS MODIFIED RESIDUE MODRES 4OVZ CSO A 271 CYS MODIFIED RESIDUE MODRES 4OVZ OCS B 112 CYS MODIFIED RESIDUE HET OCS A 112 9 HET CSO A 271 7 HET OCS B 112 9 HET ZN A 901 1 HET P85 A 902 56 HET DMS A 903 10 HET ZN B 901 1 HET P85 B 902 29 HET NA B 903 1 HET DMS B 904 10 HET DMS B 905 10 HET DMS B 906 10 HET DMS B 907 10 HETNAM OCS CYSTEINESULFONIC ACID HETNAM CSO S-HYDROXYCYSTEINE HETNAM ZN ZINC ION HETNAM P85 N-[(4-FLUOROPHENYL)METHYL]-1-[(1R)-1-NAPHTHALEN-1- HETNAM 2 P85 YLETHYL]PIPERIDINE-4-CARBOXAMIDE HETNAM DMS DIMETHYL SULFOXIDE HETNAM NA SODIUM ION FORMUL 1 OCS 2(C3 H7 N O5 S) FORMUL 1 CSO C3 H7 N O3 S FORMUL 3 ZN 2(ZN 2+) FORMUL 4 P85 2(C25 H27 F N2 O) FORMUL 5 DMS 5(C2 H6 O S) FORMUL 8 NA NA 1+ FORMUL 13 HOH *75(H2 O) HELIX 1 AA1 THR A 27 GLY A 33 1 7 HELIX 2 AA2 ASP A 62 HIS A 74 1 13 HELIX 3 AA3 SER A 79 LYS A 92 1 14 HELIX 4 AA4 ASN A 111 GLN A 122 1 12 HELIX 5 AA5 ALA A 130 ALA A 142 1 13 HELIX 6 AA6 ALA A 145 SER A 156 1 12 HELIX 7 AA7 ASP A 165 GLN A 175 1 11 HELIX 8 AA8 GLY A 202 VAL A 206 1 5 HELIX 9 AA9 SER A 213 GLY A 220 1 8 HELIX 10 AB1 ARG B 66 HIS B 74 1 9 HELIX 11 AB2 SER B 79 LYS B 92 1 14 HELIX 12 AB3 ASN B 111 GLN B 122 1 12 HELIX 13 AB4 ALA B 130 ALA B 142 1 13 HELIX 14 AB5 ALA B 145 SER B 156 1 12 HELIX 15 AB6 ASP B 165 GLN B 175 1 11 HELIX 16 AB7 GLY B 202 VAL B 206 1 5 HELIX 17 AB8 SER B 213 GLY B 220 1 8 SHEET 1 AA1 2 THR A 10 THR A 11 0 SHEET 2 AA1 2 PHE A 56 PHE A 57 1 O PHE A 56 N THR A 11 SHEET 1 AA2 2 GLN A 98 VAL A 99 0 SHEET 2 AA2 2 LEU A 102 THR A 103 -1 O LEU A 102 N VAL A 99 SHEET 1 AA3 4 GLN A 195 LEU A 200 0 SHEET 2 AA3 4 LYS A 183 VAL A 189 -1 N ARG A 184 O LEU A 200 SHEET 3 AA3 4 ALA A 231 GLU A 239 -1 O GLN A 237 N VAL A 185 SHEET 4 AA3 4 VAL A 221 ILE A 223 -1 N VAL A 221 O GLN A 233 SHEET 1 AA4 4 GLN A 195 LEU A 200 0 SHEET 2 AA4 4 LYS A 183 VAL A 189 -1 N ARG A 184 O LEU A 200 SHEET 3 AA4 4 ALA A 231 GLU A 239 -1 O GLN A 237 N VAL A 185 SHEET 4 AA4 4 SER A 310 THR A 312 -1 O TYR A 311 N GLN A 238 SHEET 1 AA5 7 MET A 207 MET A 209 0 SHEET 2 AA5 7 PHE A 242 GLN A 255 1 O SER A 246 N TYR A 208 SHEET 3 AA5 7 GLU A 296 LYS A 307 -1 O VAL A 304 N MET A 245 SHEET 4 AA5 7 CYS A 261 GLY A 267 -1 N CYS A 261 O PHE A 305 SHEET 5 AA5 7 GLY A 272 ALA A 279 -1 O HIS A 273 N THR A 266 SHEET 6 AA5 7 LEU A 283 ASP A 287 -1 O ILE A 286 N HIS A 276 SHEET 7 AA5 7 HIS A 290 MET A 294 -1 O HIS A 290 N ASP A 287 SHEET 1 AA6 2 GLN B 98 VAL B 99 0 SHEET 2 AA6 2 LEU B 102 THR B 103 -1 O LEU B 102 N VAL B 99 SHEET 1 AA7 4 THR B 197 LEU B 200 0 SHEET 2 AA7 4 LYS B 183 VAL B 189 -1 N ARG B 184 O LEU B 200 SHEET 3 AA7 4 THR B 232 GLU B 239 -1 O THR B 232 N VAL B 189 SHEET 4 AA7 4 VAL B 221 SER B 222 -1 N VAL B 221 O GLN B 233 SHEET 1 AA8 4 THR B 197 LEU B 200 0 SHEET 2 AA8 4 LYS B 183 VAL B 189 -1 N ARG B 184 O LEU B 200 SHEET 3 AA8 4 THR B 232 GLU B 239 -1 O THR B 232 N VAL B 189 SHEET 4 AA8 4 SER B 310 THR B 312 -1 O TYR B 311 N GLN B 238 SHEET 1 AA9 7 MET B 207 MET B 209 0 SHEET 2 AA9 7 PHE B 242 GLN B 255 1 O SER B 246 N TYR B 208 SHEET 3 AA9 7 GLU B 296 LYS B 307 -1 O VAL B 304 N MET B 245 SHEET 4 AA9 7 CYS B 261 GLY B 267 -1 N CYS B 261 O PHE B 305 SHEET 5 AA9 7 GLY B 272 ALA B 279 -1 O ILE B 277 N ALA B 262 SHEET 6 AA9 7 LEU B 283 ASP B 287 -1 O ILE B 286 N HIS B 276 SHEET 7 AA9 7 HIS B 290 MET B 294 -1 O THR B 292 N ARG B 285 LINK C ASN A 111 N OCS A 112 1555 1555 1.32 LINK C OCS A 112 N TYR A 113 1555 1555 1.34 LINK C GLN A 270 N CSO A 271 1555 1555 1.32 LINK C CSO A 271 N GLY A 272 1555 1555 1.33 LINK C ASN B 111 N OCS B 112 1555 1555 1.33 LINK C OCS B 112 N TYR B 113 1555 1555 1.33 LINK SG CYS A 190 ZN ZN A 901 1555 1555 2.63 LINK SG CYS A 193 ZN ZN A 901 1555 1555 2.99 LINK SG CYS A 225 ZN ZN A 901 1555 1555 2.81 LINK SG CYS A 227 ZN ZN A 901 1555 1555 2.61 LINK SG CYS B 190 ZN ZN B 901 1555 1555 2.89 LINK SG CYS B 193 ZN ZN B 901 1555 1555 2.71 LINK O LYS B 218 NA NA B 903 1555 1555 2.56 LINK SG CYS B 227 ZN ZN B 901 1555 1555 2.65 LINK O LEU B 235 NA NA B 903 1555 1555 2.72 LINK OH TYR B 311 NA NA B 903 1555 1555 2.64 LINK OG1 THR B 313 NA NA B 903 1555 1555 2.66 SITE 1 AC1 4 CYS A 190 CYS A 193 CYS A 225 CYS A 227 SITE 1 AC2 14 LEU A 163 GLY A 164 ASP A 165 PRO A 249 SITE 2 AC2 14 TYR A 265 TYR A 269 GLN A 270 TYR A 274 SITE 3 AC2 14 THR A 302 DMS A 903 MET B 209 GLY B 210 SITE 4 AC2 14 PRO B 248 TYR B 269 SITE 1 AC3 5 LYS A 158 LEU A 163 GLU A 168 P85 A 902 SITE 2 AC3 5 MET B 209 SITE 1 AC4 4 CYS B 190 CYS B 193 CYS B 225 CYS B 227 SITE 1 AC5 14 MET A 209 GLY A 210 PRO A 248 TYR A 269 SITE 2 AC5 14 LEU B 163 GLY B 164 ASP B 165 PRO B 249 SITE 3 AC5 14 TYR B 265 TYR B 269 GLN B 270 TYR B 274 SITE 4 AC5 14 THR B 302 DMS B 906 SITE 1 AC6 4 LYS B 218 LEU B 235 TYR B 311 THR B 313 SITE 1 AC7 4 GLN B 256 LEU B 260 ALA B 279 GLU B 281 SITE 1 AC8 4 THR A 199 THR A 201 GLY B 82 ARG B 83 SITE 1 AC9 6 ARG A 167 LYS B 158 GLY B 164 TYR B 269 SITE 2 AC9 6 P85 B 902 HOH B1026 SITE 1 AD1 6 TYR B 252 LYS B 253 LEU B 254 GLN B 255 SITE 2 AD1 6 THR B 258 TYR B 306 CRYST1 119.772 73.508 98.269 90.00 103.66 90.00 C 1 2 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 0.008349 0.000000 0.002029 0.00000 SCALE2 0.000000 0.013604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010472 0.00000