HEADER HYDROLASE 27-APR-06 2GTB TITLE CRYSTAL STRUCTURE OF SARS CORONAVIRUS MAIN PEPTIDASE (WITH AN TITLE 2 ADDITIONAL ALA AT THE N-TERMINUS OF EACH PROTOMER) INHIBITED BY AN TITLE 3 AZA-PEPTIDE EPOXIDE IN THE SPACE GROUP P43212 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYSTEINE PEPTIDASE, 3C-LIKE, N-FINGER, CHYMOTRYPSIN-LIKE FOLD, LONG KEYWDS 2 LOOP, ALPHA-HELICAL DOMAIN, DIMER, CATALYTIC DYAD, SPECIFICITY KEYWDS 3 POCKETS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.-W.LEE,M.M.CHERNEY,C.HUITEMA,J.LIU,K.E.JAMES,J.C.POWERS REVDAT 4 13-JUL-11 2GTB 1 VERSN REVDAT 3 24-FEB-09 2GTB 1 VERSN REVDAT 2 06-FEB-07 2GTB 1 JRNL REVDAT 1 26-DEC-06 2GTB 0 JRNL AUTH T.W.LEE,M.M.CHERNEY,J.LIU,K.E.JAMES,J.C.POWERS,L.D.ELTIS, JRNL AUTH 2 M.N.G.JAMES JRNL TITL CRYSTAL STRUCTURES REVEAL AN INDUCED-FIT BINDING OF A JRNL TITL 2 SUBSTRATE-LIKE AZA-PEPTIDE EPOXIDE TO SARS CORONAVIRUS MAIN JRNL TITL 3 PEPTIDASE. JRNL REF J.MOL.BIOL. V. 366 916 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17196984 JRNL DOI 10.1016/J.JMB.2006.11.078 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17168 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 923 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1244 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2320 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.93000 REMARK 3 B22 (A**2) : -1.93000 REMARK 3 B33 (A**2) : 3.86000 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): 0.237 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.210 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.492 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2431 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3299 ; 2.064 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 298 ; 8.103 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;38.409 ;24.037 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 390 ;18.620 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;19.569 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 369 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1861 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1101 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1619 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 114 ; 0.174 ; 0.200 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): 82 ; 0.265 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.177 ; 0.200 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): 1533 ; 1.046 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2410 ; 1.571 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1020 ; 2.744 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 889 ; 3.660 ; 4.500 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 300 REMARK 3 ORIGIN FOR THE GROUP (A): 6.5270 -0.1880 12.7010 REMARK 3 T TENSOR REMARK 3 T11: -0.0237 T22: -0.0682 REMARK 3 T33: -0.1095 T12: 0.0028 REMARK 3 T13: -0.0188 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 3.7377 L22: 0.7530 REMARK 3 L33: 0.4146 L12: 0.5128 REMARK 3 L13: -0.1634 L23: -0.1212 REMARK 3 S TENSOR REMARK 3 S11: 0.0365 S12: 0.0478 S13: 0.0093 REMARK 3 S21: 0.0190 S22: -0.0120 S23: 0.0727 REMARK 3 S31: 0.0377 S32: 0.0108 S33: -0.0245 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 401 A 401 REMARK 3 ORIGIN FOR THE GROUP (A): 18.3770 -12.0960 11.1630 REMARK 3 T TENSOR REMARK 3 T11: 0.0056 T22: 0.0047 REMARK 3 T33: 0.0040 T12: 0.0081 REMARK 3 T13: -0.0137 T23: -0.0081 REMARK 3 L TENSOR REMARK 3 L11: 24.7933 L22: 10.8498 REMARK 3 L33: 20.0755 L12: -16.3970 REMARK 3 L13: 13.8317 L23: -9.4117 REMARK 3 S TENSOR REMARK 3 S11: -0.7745 S12: 0.3434 S13: -0.5905 REMARK 3 S21: -0.2723 S22: 0.2792 S23: -1.0401 REMARK 3 S31: 0.1207 S32: -0.6221 S33: 0.4953 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 2GTB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-06. REMARK 100 THE RCSB ID CODE IS RCSB037523. 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) : NULL 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) : 1.116 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 : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18098 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM AMMONIUM ACETATE, 6% PEG 8000, 3% REMARK 280 ETHYLENE GLYCOL, 1MM DITHIOTHREITOL, 0.1 MES (PH 6.5), VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 51.93100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.04350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.04350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.89650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.04350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.04350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.96550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.04350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.04350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 77.89650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.04350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.04350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.96550 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.93100 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 300 REMARK: THE PROTOMER IN THE ASYMMETRIC UNIT X,Y,Z FORMS THE REMARK 300 BIOLOGICAL UNIT OF SARS CORONAVIRUS MAIN PEPTIDASE (A HOMODIMER) REMARK 300 WITH THAT IN THE ASYMMETRIC UNIT -Y,-X,0.5-Z. 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 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 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 51.93100 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 SER A 1 REMARK 465 SER A 301 REMARK 465 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 REMARK 465 GLN A 306 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 CYS A 44 CB CYS A 44 SG -0.098 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 ASP A 92 CB - CA - C ANGL. DEV. = -13.6 DEGREES REMARK 500 ASP A 289 CB - CG - OD2 ANGL. DEV. = 5.5 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 ASP A 33 -131.49 57.24 REMARK 500 ASN A 84 -119.66 46.79 REMARK 500 ASP A 92 -44.56 -12.39 REMARK 500 TYR A 154 -98.44 40.03 REMARK 500 HIS A 164 -54.51 -121.55 REMARK 500 PRO A 184 25.48 -76.94 REMARK 500 GLN A 189 53.72 -98.13 REMARK 500 GLN A 192 -158.94 -120.77 REMARK 500 ASN A 277 89.56 -5.03 REMARK 500 ILE A 286 143.10 62.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ILE A 286 24.2 L L OUTSIDE RANGE 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 A 524 DISTANCE = 5.18 ANGSTROMS 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GT7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS CORONAVIRUS MAIN PEPTIDASE AT PH REMARK 900 6.0 IN THE SPACE GROUP P21 REMARK 900 RELATED ID: 2GT8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS CORONAVIRUS MAIN PEPTIDASE (WITH REMARK 900 AN ADDITIONAL ALA AT THE N-TERMINUS OF EACH PROTOMER) IN REMARK 900 THE SPACE GROUP P43212 DBREF 2GTB A 1 306 UNP P59641 R1AB_CVHSA 3241 3546 SEQADV 2GTB ALA A 0 UNP P59641 INSERTION 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 HET AZP A 401 46 HET ACY A 402 4 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 HETNAM ACY ACETIC ACID FORMUL 2 AZP C32 H43 N5 O9 FORMUL 3 ACY C2 H4 O2 FORMUL 4 HOH *127(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 THR A 45 MET A 49 5 5 HELIX 4 4 ASN A 53 ARG A 60 1 8 HELIX 5 5 SER A 62 HIS A 64 5 3 HELIX 6 6 ILE A 200 GLY A 215 1 16 HELIX 7 7 THR A 226 LYS A 236 1 11 HELIX 8 8 THR A 243 LEU A 250 1 8 HELIX 9 9 LEU A 250 GLY A 258 1 9 HELIX 10 10 ALA A 260 ASN A 274 1 15 HELIX 11 11 THR A 292 CYS A 300 1 9 SHEET 1 A 7 VAL A 73 LEU A 75 0 SHEET 2 A 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75 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 THR A 25 N CYS A 22 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 SER A 123 N ALA A 116 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 LINK SG CYS A 145 CBM AZP A 401 1555 1555 2.15 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 PRO A 168 SITE 5 AC1 26 HIS A 172 ASP A 187 ARG A 188 GLN A 189 SITE 6 AC1 26 GLN A 192 ALA A 193 LYS A 236 TYR A 237 SITE 7 AC1 26 GLN A 273 HOH A 424 SITE 1 AC2 5 LYS A 5 ALA A 7 VAL A 125 TYR A 126 SITE 2 AC2 5 GLN A 127 CRYST1 70.087 70.087 103.862 90.00 90.00 90.00 P 43 21 2 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 0.014268 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014268 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009628 0.00000