HEADER VIRAL PROTEIN 12-APR-10 3MJ5 TITLE SEVERE ACUTE RESPIRATORY SYNDROME-CORONAVIRUS PAPAIN-LIKE PROTEASE TITLE 2 INHIBITORS: DESIGN, SYNTHESIS, PROTEIN-LIGAND X-RAY STRUCTURE AND TITLE 3 BIOLOGICAL EVALUATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICASE POLYPROTEIN 1A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SARS POLYPROTEIN RESIDUES 1544-1855; COMPND 5 SYNONYM: PP1A, ORF1A POLYPROTEIN, NON-STRUCTURAL PROTEIN 1, NSP1, COMPND 6 LEADER PROTEIN, NON-STRUCTURAL PROTEIN 2, NSP2, P65 HOMOLOG, NON- COMPND 7 STRUCTURAL PROTEIN 3, NSP3, PAPAIN-LIKE PROTEINASE, PL-PRO, PL2-PRO, COMPND 8 NON-STRUCTURAL PROTEIN 4, NSP4, 3C-LIKE PROTEINASE, 3CL-PRO, 3CLP, COMPND 9 NSP5, NON-STRUCTURAL PROTEIN 6, NSP6, NON-STRUCTURAL PROTEIN 7, NSP7, COMPND 10 NON-STRUCTURAL PROTEIN 8, NSP8, NON-STRUCTURAL PROTEIN 9, NSP9, NON- COMPND 11 STRUCTURAL PROTEIN 10, NSP10, GROWTH FACTOR-LIKE PEPTIDE, GFL, NON- COMPND 12 STRUCTURAL PROTEIN 11, NSP11; COMPND 13 EC: 3.4.22.-; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS; SOURCE 3 ORGANISM_COMMON: SARS-COV; SOURCE 4 ORGANISM_TAXID: 227859; SOURCE 5 STRAIN: URBANI; SOURCE 6 GENE: 1A, ORF1 (NSP3) RESIDUES 1544-1855; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS NON-COVALENT INHIBITOR, CYSTEINE PROTEASE, SARS CORONAVIRUS, ZINC- KEYWDS 2 FINGER, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.D.MESECAR,K.M.RATIA,S.D.PEGAN REVDAT 5 20-NOV-24 3MJ5 1 REMARK REVDAT 4 13-MAR-24 3MJ5 1 COMPND SOURCE REVDAT 3 06-SEP-23 3MJ5 1 REMARK SEQADV LINK REVDAT 2 14-JUL-10 3MJ5 1 JRNL REVDAT 1 30-JUN-10 3MJ5 0 JRNL AUTH A.K.GHOSH,J.TAKAYAMA,K.V.RAO,K.RATIA,R.CHAUDHURI, JRNL AUTH 2 D.C.MULHEARN,H.LEE,D.B.NICHOLS,S.BALIJI,S.C.BAKER, JRNL AUTH 3 M.E.JOHNSON,A.D.MESECAR JRNL TITL SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS PAPAIN-LIKE JRNL TITL 2 NOVEL PROTEASE INHIBITORS: DESIGN, SYNTHESIS, PROTEIN-LIGAND JRNL TITL 3 X-RAY STRUCTURE AND BIOLOGICAL EVALUATION JRNL REF J.MED.CHEM. V. 53 4968 2010 JRNL REFN ISSN 0022-2623 JRNL PMID 20527968 JRNL DOI 10.1021/JM1004489 REMARK 2 REMARK 2 RESOLUTION. 2.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 94.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 22215 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1184 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1270 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4523 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.21000 REMARK 3 B22 (A**2) : 10.74000 REMARK 3 B33 (A**2) : -12.95000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -6.32000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.141 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.180 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.816 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4694 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6372 ; 1.406 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 572 ; 5.745 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 206 ;39.131 ;24.417 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 778 ;17.141 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;16.355 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 714 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3526 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2849 ; 0.714 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4596 ; 1.361 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1845 ; 1.803 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1776 ; 3.030 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3MJ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23605 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.370 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.180 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 2FE8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DIFFRACTION-QUALITY CRYSTALS GREW FROM REMARK 280 A SITTING DROP CONTAINING 5 MG/ML PLPRO, 1 MM INHIBITOR, 1 M REMARK 280 (NH4)2SO4, 50 MM MES, PH 6.5, AND 2.5% PEG 400., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K 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 59.19850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.06450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.19850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.06450 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, 3 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 300 REMARK: MONOMER OF PLPRO BOUND TO INHIBITOR 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR B 84 ND2 ASN B 147 1.89 REMARK 500 CD1 ILE A 6 OE1 GLU A 52 1.96 REMARK 500 O GLN B 255 OG1 THR B 258 2.07 REMARK 500 OE2 GLU A 162 OE2 GLU B 204 2.08 REMARK 500 OE2 GLU A 281 OH TYR A 284 2.17 REMARK 500 N HIS A 48 ND1 HIS A 51 2.19 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 VAL A 42 24.24 -146.15 REMARK 500 VAL A 49 -17.76 -45.81 REMARK 500 GLU A 52 171.32 -52.05 REMARK 500 PRO A 60 86.56 -61.40 REMARK 500 HIS A 74 34.10 72.10 REMARK 500 ALA A 108 139.31 -173.87 REMARK 500 HIS A 192 -64.87 -99.36 REMARK 500 VAL A 226 -17.42 -41.93 REMARK 500 ARG A 229 -169.74 -111.36 REMARK 500 LYS A 280 -138.30 -112.43 REMARK 500 THR A 309 -69.63 -131.35 REMARK 500 PHE B 96 79.70 -111.35 REMARK 500 LYS B 191 -71.60 -54.18 REMARK 500 HIS B 192 -77.71 -79.79 REMARK 500 LYS B 196 131.02 -172.40 REMARK 500 VAL B 226 -73.75 -31.00 REMARK 500 LYS B 280 -124.03 -121.26 REMARK 500 ASP B 287 76.59 -116.61 REMARK 500 THR B 309 -61.90 -131.91 REMARK 500 THR B 313 174.94 -56.51 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 ILE B 315 LYS B 316 144.66 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 ZN A 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 190 SG REMARK 620 2 CYS A 193 SG 114.2 REMARK 620 3 CYS A 225 SG 106.2 95.9 REMARK 620 4 CYS A 227 SG 99.7 120.7 120.2 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 60.6 REMARK 620 3 CYS B 225 SG 99.8 140.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GRM A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GRM B 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FE8 RELATED DB: PDB REMARK 900 APO SARS PLPRO REMARK 900 RELATED ID: 3E9S RELATED DB: PDB REMARK 900 SARS PLPRO COMPLEXED WITH NONCOVALENT INHIBITOR DBREF 3MJ5 A 2 316 UNP P0C6U8 R1A_CVHSA 1541 1855 DBREF 3MJ5 B 2 316 UNP P0C6U8 R1A_CVHSA 1541 1855 SEQADV 3MJ5 MET A 1 UNP P0C6U8 EXPRESSION TAG SEQADV 3MJ5 MET B 1 UNP P0C6U8 EXPRESSION TAG 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 CYS 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 CYS 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 CYS 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 HET GRM A 801 31 HET ZN A 901 1 HET GRM B 801 31 HET ZN B 901 1 HETNAM GRM N-(1,3-BENZODIOXOL-5-YLMETHYL)-1-[(1R)-1-NAPHTHALEN-1- HETNAM 2 GRM YLETHYL]PIPERIDINE-4-CARBOXAMIDE HETNAM ZN ZINC ION FORMUL 3 GRM 2(C26 H28 N2 O3) FORMUL 4 ZN 2(ZN 2+) FORMUL 7 HOH *119(H2 O) HELIX 1 1 THR A 27 PHE A 32 1 6 HELIX 2 2 ASP A 62 HIS A 74 1 13 HELIX 3 3 SER A 79 LYS A 92 1 14 HELIX 4 4 ASN A 111 GLN A 122 1 12 HELIX 5 5 ALA A 130 ARG A 141 1 12 HELIX 6 6 ALA A 145 SER A 156 1 12 HELIX 7 7 ASP A 165 GLN A 175 1 11 HELIX 8 8 GLY A 202 VAL A 206 1 5 HELIX 9 9 SER A 213 GLY A 220 1 8 HELIX 10 10 ASP B 62 HIS B 74 1 13 HELIX 11 11 SER B 79 LYS B 92 1 14 HELIX 12 12 ASN B 111 GLN B 122 1 12 HELIX 13 13 ALA B 130 ALA B 142 1 13 HELIX 14 14 ALA B 145 SER B 156 1 12 HELIX 15 15 ASP B 165 LEU B 174 1 10 HELIX 16 16 GLN B 175 ALA B 177 5 3 HELIX 17 17 GLY B 202 VAL B 206 1 5 HELIX 18 18 SER B 213 GLY B 220 1 8 SHEET 1 A 5 HIS A 18 VAL A 22 0 SHEET 2 A 5 ILE A 6 THR A 11 -1 N ILE A 6 O VAL A 22 SHEET 3 A 5 THR A 55 VAL A 58 1 O PHE A 56 N PHE A 9 SHEET 4 A 5 THR A 35 LEU A 37 -1 N TYR A 36 O PHE A 57 SHEET 5 A 5 ALA A 40 ASP A 41 -1 O ALA A 40 N LEU A 37 SHEET 1 B 2 GLN A 98 VAL A 99 0 SHEET 2 B 2 LEU A 102 THR A 103 -1 O LEU A 102 N VAL A 99 SHEET 1 C 4 GLY A 194 THR A 201 0 SHEET 2 C 4 LYS A 183 CYS A 190 -1 N ARG A 184 O LEU A 200 SHEET 3 C 4 ARG A 229 GLU A 239 -1 O THR A 232 N VAL A 189 SHEET 4 C 4 VAL A 221 CYS A 225 -1 N ILE A 223 O ALA A 231 SHEET 1 D 4 GLY A 194 THR A 201 0 SHEET 2 D 4 LYS A 183 CYS A 190 -1 N ARG A 184 O LEU A 200 SHEET 3 D 4 ARG A 229 GLU A 239 -1 O THR A 232 N VAL A 189 SHEET 4 D 4 SER A 310 THR A 312 -1 O TYR A 311 N GLN A 238 SHEET 1 E 7 MET A 207 MET A 209 0 SHEET 2 E 7 PHE A 242 GLN A 255 1 O SER A 246 N TYR A 208 SHEET 3 E 7 GLU A 296 LYS A 307 -1 O TYR A 297 N LEU A 254 SHEET 4 E 7 CYS A 261 GLY A 267 -1 N CYS A 261 O PHE A 305 SHEET 5 E 7 GLY A 272 ALA A 279 -1 O ILE A 277 N ALA A 262 SHEET 6 E 7 LEU A 283 ASP A 287 -1 O TYR A 284 N THR A 278 SHEET 7 E 7 HIS A 290 MET A 294 -1 O THR A 292 N ARG A 285 SHEET 1 F 2 GLN B 98 VAL B 99 0 SHEET 2 F 2 LEU B 102 THR B 103 -1 O LEU B 102 N VAL B 99 SHEET 1 G 4 GLN B 195 LEU B 200 0 SHEET 2 G 4 LYS B 183 VAL B 189 -1 N ARG B 184 O LEU B 200 SHEET 3 G 4 ASP B 230 GLU B 239 -1 O VAL B 236 N VAL B 185 SHEET 4 G 4 VAL B 221 PRO B 224 -1 N ILE B 223 O ALA B 231 SHEET 1 H 4 GLN B 195 LEU B 200 0 SHEET 2 H 4 LYS B 183 VAL B 189 -1 N ARG B 184 O LEU B 200 SHEET 3 H 4 ASP B 230 GLU B 239 -1 O VAL B 236 N VAL B 185 SHEET 4 H 4 SER B 310 THR B 312 -1 O TYR B 311 N GLN B 238 SHEET 1 I 7 MET B 207 MET B 209 0 SHEET 2 I 7 PHE B 242 GLN B 255 1 O SER B 246 N TYR B 208 SHEET 3 I 7 GLU B 296 LYS B 307 -1 O TYR B 297 N LEU B 254 SHEET 4 I 7 CYS B 261 ASN B 268 -1 N CYS B 261 O PHE B 305 SHEET 5 I 7 CYS B 271 ALA B 279 -1 O ILE B 277 N ALA B 262 SHEET 6 I 7 LEU B 283 ASP B 287 -1 O TYR B 284 N THR B 278 SHEET 7 I 7 HIS B 290 MET B 294 -1 O THR B 292 N ARG B 285 SSBOND 1 CYS B 190 CYS B 193 1555 1555 2.48 LINK SG CYS A 190 ZN ZN A 901 1555 1555 2.36 LINK SG CYS A 193 ZN ZN A 901 1555 1555 2.18 LINK SG CYS A 225 ZN ZN A 901 1555 1555 2.08 LINK SG CYS A 227 ZN ZN A 901 1555 1555 2.49 LINK SG CYS B 190 ZN ZN B 901 1555 1555 2.57 LINK SG CYS B 193 ZN ZN B 901 1555 1555 2.32 LINK SG CYS B 225 ZN ZN B 901 1555 1555 2.55 SITE 1 AC1 12 LEU A 163 GLY A 164 ASP A 165 PRO A 248 SITE 2 AC1 12 PRO A 249 TYR A 269 GLN A 270 TYR A 274 SITE 3 AC1 12 THR A 302 MET B 209 GLY B 210 PRO B 248 SITE 1 AC2 4 CYS A 190 CYS A 193 CYS A 225 CYS A 227 SITE 1 AC3 11 MET A 209 GLY A 210 PRO A 248 TYR A 269 SITE 2 AC3 11 GLY B 164 ASP B 165 PRO B 249 TYR B 265 SITE 3 AC3 11 TYR B 269 TYR B 274 THR B 302 SITE 1 AC4 5 CYS B 190 HIS B 192 CYS B 193 CYS B 225 SITE 2 AC4 5 CYS B 227 CRYST1 118.397 74.129 96.895 90.00 103.02 90.00 C 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008446 0.000000 0.001953 0.00000 SCALE2 0.000000 0.013490 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010593 0.00000