HEADER HYDROLASE 30-JUN-05 2A5K TITLE CRYSTAL STRUCTURES OF SARS CORONAVIRUS MAIN PEPTIDASE INHIBITED BY AN TITLE 2 AZA-PEPTIDE EPOXIDE IN SPACE GROUP P212121 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3CL-PRO, 3CLP, NSP2; COMPND 5 EC: 3.4.22.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS; SOURCE 3 ORGANISM_TAXID: 227859; SOURCE 4 STRAIN: SARS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: GJ1158; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PT7HSP2 KEYWDS CYSTEINE PEPTIDASE, 3C-LIKE, N-FINGER, CHYMOTRYPSIN-LIKE FOLD, LONG KEYWDS 2 LOOP, ALPHA-HELICAL DOMAIN, DIMER, CATALYTIC DYAD, SPECIFICITY KEYWDS 3 POCKETS, AZA-PEPTIDE EPOXIDE, SUBSTRATE-LIKE INHIBITOR, C-S COVALENT KEYWDS 4 BOND, EPOXIDE STEREOCHEMISTRY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.-W.LEE,M.M.CHERNEY,C.HUITEMA,J.LIU,K.E.JAMES,J.C.POWERS,L.D.ELTIS, AUTHOR 2 M.N.JAMES REVDAT 5 13-NOV-24 2A5K 1 REMARK REVDAT 4 23-AUG-23 2A5K 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2A5K 1 VERSN REVDAT 2 01-NOV-05 2A5K 1 JRNL REVDAT 1 25-OCT-05 2A5K 0 JRNL AUTH T.-W.LEE,M.M.CHERNEY,C.HUITEMA,J.LIU,K.E.JAMES,J.C.POWERS, JRNL AUTH 2 L.D.ELTIS,M.N.JAMES JRNL TITL CRYSTAL STRUCTURES OF THE MAIN PEPTIDASE FROM THE SARS JRNL TITL 2 CORONAVIRUS INHIBITED BY A SUBSTRATE-LIKE AZA-PEPTIDE JRNL TITL 3 EPOXIDE JRNL REF J.MOL.BIOL. V. 353 1137 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16219322 JRNL DOI 10.1016/J.JMB.2005.09.004 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 31565 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1684 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2153 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4676 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 278 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.01000 REMARK 3 B22 (A**2) : -1.27000 REMARK 3 B33 (A**2) : -1.74000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.283 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.237 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.506 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5009 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6798 ; 1.944 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 612 ; 7.517 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 230 ;37.716 ;23.913 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 825 ;18.855 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;22.179 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 758 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3833 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2347 ; 0.254 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3428 ; 0.333 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 479 ; 0.236 ; 0.500 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): 46 ; 0.292 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.284 ; 0.500 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): 3113 ; 1.602 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4946 ; 2.529 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2123 ; 1.616 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1852 ; 2.285 ; 3.000 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2A5K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000033514. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-AUG-04 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 : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115869 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33305 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2A5A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACETATE, PEG 8000, ETHYLENE REMARK 280 GLYCOL, DITHIOTHREITOL, MES, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 32.67650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.66100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.73900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 83.66100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.67650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.73900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC 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 ALA A 0 REMARK 465 PHE A 305 REMARK 465 GLN A 306 REMARK 465 ALA B 0 REMARK 465 SER B 301 REMARK 465 GLY B 302 REMARK 465 VAL B 303 REMARK 465 THR B 304 REMARK 465 PHE B 305 REMARK 465 GLN B 306 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 372 O HOH A 374 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 THR B 224 C THR B 224 O 0.118 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 LEU A 67 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 CYS A 128 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 LEU A 167 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG B 4 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 LEU B 87 CB - CG - CD1 ANGL. DEV. = -10.3 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 ASP A 33 -129.94 49.00 REMARK 500 ASN A 51 62.25 -159.18 REMARK 500 ASN A 84 -121.36 47.69 REMARK 500 TYR A 154 -108.03 65.24 REMARK 500 PRO A 184 35.10 -82.97 REMARK 500 THR A 285 -158.35 -81.59 REMARK 500 ILE A 286 130.83 53.94 REMARK 500 ILE A 286 130.83 90.83 REMARK 500 ASP B 33 -122.18 46.22 REMARK 500 ASN B 84 -121.34 50.52 REMARK 500 TYR B 154 -71.14 54.85 REMARK 500 PRO B 184 38.01 -89.93 REMARK 500 GLN B 192 141.71 -178.18 REMARK 500 ASN B 214 0.21 -60.17 REMARK 500 ARG B 217 -5.81 -149.37 REMARK 500 ARG B 279 -179.16 -63.82 REMARK 500 ARG B 279 178.53 -53.93 REMARK 500 ILE B 286 139.36 56.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN BEFORE BINDING TO THE PEPTIDASE, CBM, CBO AND OBN FORM REMARK 600 AN EPOXIDE RING IN AZP. UPON BINDING TO THE PEPTIDASE, CYS145 SG REMARK 600 NUCLEOPHILLICALLY ATTACKS CBM, RESULTING IN THE OPENING OF THE REMARK 600 RING AND THE INVERSION OF THE CONFIGURATIONS OF CBM AND CBO. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZP A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZP B 307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2A5A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS CORONAVIRUS MAIN PEPTIDASE UNBOUND IN THE REMARK 900 CRYSTAL FORM C2 REMARK 900 RELATED ID: 2A5I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS CORONAVIRUS MAIN PEPTIDASE INHIBITED BY REMARK 900 AN AZA-PEPTIDE EPOXIDE IN THE CRYSTAL FORM C2 DBREF 2A5K A 1 306 UNP P59641 R1AB_CVHSA 3241 3546 DBREF 2A5K B 1 306 UNP P59641 R1AB_CVHSA 3241 3546 SEQADV 2A5K ALA A 0 UNP P59641 EXPRESSION TAG SEQADV 2A5K ALA B 0 UNP P59641 EXPRESSION TAG SEQRES 1 A 307 ALA SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS SEQRES 2 A 307 VAL GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR SEQRES 3 A 307 THR LEU ASN GLY LEU TRP LEU ASP ASP THR VAL TYR CYS SEQRES 4 A 307 PRO ARG HIS VAL ILE CYS THR ALA GLU ASP MET LEU ASN SEQRES 5 A 307 PRO ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS SEQRES 6 A 307 SER PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL SEQRES 7 A 307 ILE GLY HIS SER MET GLN ASN CYS LEU LEU ARG LEU LYS SEQRES 8 A 307 VAL ASP THR SER ASN PRO LYS THR PRO LYS TYR LYS PHE SEQRES 9 A 307 VAL ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA SEQRES 10 A 307 CYS TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA SEQRES 11 A 307 MET ARG PRO ASN HIS THR ILE LYS GLY SER PHE LEU ASN SEQRES 12 A 307 GLY SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP SEQRES 13 A 307 CYS VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO SEQRES 14 A 307 THR GLY VAL HIS ALA GLY THR ASP LEU GLU GLY LYS PHE SEQRES 15 A 307 TYR GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA SEQRES 16 A 307 GLY THR ASP THR THR ILE THR LEU ASN VAL LEU ALA TRP SEQRES 17 A 307 LEU TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU SEQRES 18 A 307 ASN ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL SEQRES 19 A 307 ALA MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS SEQRES 20 A 307 VAL ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE SEQRES 21 A 307 ALA VAL LEU ASP MET CYS ALA ALA LEU LYS GLU LEU LEU SEQRES 22 A 307 GLN ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER THR SEQRES 23 A 307 ILE LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG SEQRES 24 A 307 GLN CYS SER GLY VAL THR PHE GLN SEQRES 1 B 307 ALA SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS SEQRES 2 B 307 VAL GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR SEQRES 3 B 307 THR LEU ASN GLY LEU TRP LEU ASP ASP THR VAL TYR CYS SEQRES 4 B 307 PRO ARG HIS VAL ILE CYS THR ALA GLU ASP MET LEU ASN SEQRES 5 B 307 PRO ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS SEQRES 6 B 307 SER PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL SEQRES 7 B 307 ILE GLY HIS SER MET GLN ASN CYS LEU LEU ARG LEU LYS SEQRES 8 B 307 VAL ASP THR SER ASN PRO LYS THR PRO LYS TYR LYS PHE SEQRES 9 B 307 VAL ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA SEQRES 10 B 307 CYS TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA SEQRES 11 B 307 MET ARG PRO ASN HIS THR ILE LYS GLY SER PHE LEU ASN SEQRES 12 B 307 GLY SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP SEQRES 13 B 307 CYS VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO SEQRES 14 B 307 THR GLY VAL HIS ALA GLY THR ASP LEU GLU GLY LYS PHE SEQRES 15 B 307 TYR GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA SEQRES 16 B 307 GLY THR ASP THR THR ILE THR LEU ASN VAL LEU ALA TRP SEQRES 17 B 307 LEU TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU SEQRES 18 B 307 ASN ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL SEQRES 19 B 307 ALA MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS SEQRES 20 B 307 VAL ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE SEQRES 21 B 307 ALA VAL LEU ASP MET CYS ALA ALA LEU LYS GLU LEU LEU SEQRES 22 B 307 GLN ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER THR SEQRES 23 B 307 ILE LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG SEQRES 24 B 307 GLN CYS SER GLY VAL THR PHE GLN HET AZP A 307 46 HET AZP B 307 46 HETNAM AZP (5S,8S,14R)-ETHYL 11-(3-AMINO-3-OXOPROPYL)-8-BENZYL-14- HETNAM 2 AZP HYDROXY-5-ISOBUTYL-3,6,9,12-TETRAOXO-1-PHENYL-2-OXA-4, HETNAM 3 AZP 7,10,11-TETRAAZAPENTADECAN-15-OATE FORMUL 3 AZP 2(C32 H43 N5 O9) FORMUL 5 HOH *278(H2 O) HELIX 1 1 SER A 10 GLY A 15 1 6 HELIX 2 2 HIS A 41 CYS A 44 5 4 HELIX 3 3 ASN A 53 ARG A 60 1 8 HELIX 4 4 SER A 62 PHE A 66 5 5 HELIX 5 5 ILE A 200 ASN A 214 1 15 HELIX 6 6 THR A 226 TYR A 237 1 12 HELIX 7 7 THR A 243 LEU A 250 1 8 HELIX 8 8 LEU A 250 GLY A 258 1 9 HELIX 9 9 ALA A 260 GLY A 275 1 16 HELIX 10 10 THR A 292 GLY A 302 1 11 HELIX 11 11 SER B 10 GLY B 15 1 6 HELIX 12 12 HIS B 41 CYS B 44 5 4 HELIX 13 13 THR B 45 MET B 49 5 5 HELIX 14 14 ASN B 53 LYS B 61 1 9 HELIX 15 15 SER B 62 PHE B 66 5 5 HELIX 16 16 ILE B 200 GLY B 215 1 16 HELIX 17 17 THR B 226 TYR B 237 1 12 HELIX 18 18 THR B 243 LEU B 250 1 8 HELIX 19 19 LEU B 250 GLY B 258 1 9 HELIX 20 20 ALA B 260 GLY B 275 1 16 HELIX 21 21 THR B 292 GLN B 299 1 8 SHEET 1 A 7 VAL A 73 LEU A 75 0 SHEET 2 A 7 LEU A 67 ALA A 70 -1 N ALA A 70 O VAL A 73 SHEET 3 A 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67 SHEET 4 A 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 5 A 7 THR A 35 PRO A 39 -1 O TYR A 37 N LEU A 30 SHEET 6 A 7 LEU A 86 VAL A 91 -1 O LEU A 89 N VAL A 36 SHEET 7 A 7 VAL A 77 GLN A 83 -1 N GLN A 83 O LEU A 86 SHEET 1 B 5 TYR A 101 PHE A 103 0 SHEET 2 B 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 B 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158 SHEET 4 B 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 B 5 SER A 121 ALA A 129 -1 O TYR A 126 N VAL A 114 SHEET 1 C 3 TYR A 101 PHE A 103 0 SHEET 2 C 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 C 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 SHEET 1 D 7 VAL B 73 LEU B 75 0 SHEET 2 D 7 LEU B 67 ALA B 70 -1 N ALA B 70 O VAL B 73 SHEET 3 D 7 MET B 17 CYS B 22 -1 N THR B 21 O LEU B 67 SHEET 4 D 7 THR B 25 LEU B 32 -1 O GLY B 29 N VAL B 18 SHEET 5 D 7 THR B 35 PRO B 39 -1 O TYR B 37 N LEU B 30 SHEET 6 D 7 LEU B 86 VAL B 91 -1 O LEU B 87 N CYS B 38 SHEET 7 D 7 VAL B 77 GLN B 83 -1 N ILE B 78 O LYS B 90 SHEET 1 E 5 TYR B 101 PHE B 103 0 SHEET 2 E 5 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 102 SHEET 3 E 5 VAL B 148 ASP B 153 -1 N ASN B 151 O SER B 158 SHEET 4 E 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150 SHEET 5 E 5 SER B 121 ALA B 129 -1 O TYR B 126 N VAL B 114 SHEET 1 F 3 TYR B 101 PHE B 103 0 SHEET 2 F 3 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 102 SHEET 3 F 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 LINK SG CYS A 145 CBM AZP A 307 1555 1555 2.09 LINK SG CYS B 145 CBM AZP B 307 1555 1555 2.05 SITE 1 AC1 26 THR A 25 HIS A 41 MET A 49 TYR A 54 SITE 2 AC1 26 PHE A 140 LEU A 141 ASN A 142 GLY A 143 SITE 3 AC1 26 SER A 144 CYS A 145 HIS A 163 HIS A 164 SITE 4 AC1 26 MET A 165 GLU A 166 LEU A 167 HIS A 172 SITE 5 AC1 26 PHE A 185 ASP A 187 ARG A 188 GLN A 189 SITE 6 AC1 26 THR A 190 GLN A 192 LYS A 236 HOH A 328 SITE 7 AC1 26 HOH A 348 HOH A 397 SITE 1 AC2 21 THR B 25 HIS B 41 MET B 49 TYR B 54 SITE 2 AC2 21 PHE B 140 LEU B 141 ASN B 142 GLY B 143 SITE 3 AC2 21 SER B 144 CYS B 145 HIS B 163 HIS B 164 SITE 4 AC2 21 MET B 165 GLU B 166 PRO B 168 HIS B 172 SITE 5 AC2 21 ASP B 187 ARG B 188 GLN B 189 THR B 190 SITE 6 AC2 21 ALA B 191 CRYST1 65.353 67.478 167.322 90.00 90.00 90.00 P 21 21 21 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 0.015302 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005977 0.00000