HEADER HYDROLASE 22-JUL-05 2BX3 TITLE CRYSTAL STRUCTURE OF SARS CORONAVIRUS MAIN PROTEINASE (P43212) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE NSP5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 3241-3546; COMPND 5 SYNONYM: 3CL-PRO,3CLP,MAIN PROTEASE,MPRO,NON-STRUCTURAL PROTEIN 5, COMPND 6 NSP5,SARS CORONAVIRUS MAIN PROTEINASE; COMPND 7 EC: 3.4.22.69; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS SIN2774; SOURCE 3 ORGANISM_TAXID: 235410; SOURCE 4 GENE: 1A; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: TUNER (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS SARS, HYDROLASE, ANTI-PARALLEL B-BARREL, ANTI-PARALLEL A- HELICES, KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.H.G.VERSCHUEREN,J.R.MESTERS,R.HILGENFELD REVDAT 8 31-JAN-24 2BX3 1 REMARK REVDAT 7 07-DEC-22 2BX3 1 COMPND SOURCE DBREF REVDAT 6 24-JUL-19 2BX3 1 REMARK REVDAT 5 13-JUL-11 2BX3 1 VERSN REVDAT 4 24-FEB-09 2BX3 1 VERSN REVDAT 3 19-SEP-06 2BX3 1 SEQRES REVDAT 2 02-NOV-05 2BX3 1 AUTHOR JRNL REVDAT 1 26-SEP-05 2BX3 0 JRNL AUTH J.TAN,K.H.G.VERSCHUEREN,K.ANAND,J.SHEN,M.YANG,Y.XU,Z.RAO, JRNL AUTH 2 J.BIGALKE,B.HEISEN,J.R.MESTERS,K.CHEN,X.SHEN,H.JIANG, JRNL AUTH 3 R.HILGENFELD JRNL TITL PH-DEPENDENT CONFORMATIONAL FLEXIBILITY OF THE SARS-COV MAIN JRNL TITL 2 PROTEINASE (M(PRO)) DIMER: MOLECULAR DYNAMICS SIMULATIONS JRNL TITL 3 AND MULTIPLE X-RAY STRUCTURE ANALYSES. JRNL REF J.MOL.BIOL. V. 354 25 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16242152 JRNL DOI 10.1016/J.JMB.2005.09.012 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16395 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 884 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) : 1182 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2326 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 259 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 20.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.77000 REMARK 3 B22 (A**2) : -1.77000 REMARK 3 B33 (A**2) : 3.54000 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): 0.244 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.211 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.146 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.262 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2477 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2184 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3372 ; 1.718 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5110 ; 0.818 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 318 ; 9.207 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;34.603 ;24.298 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 410 ;16.821 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;21.846 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 377 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2802 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 512 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 579 ; 0.229 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2429 ; 0.209 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1226 ; 0.197 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 1548 ; 0.099 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 315 ; 0.290 ; 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): 49 ; 0.300 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 124 ; 0.267 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 32 ; 0.307 ; 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): 1905 ; 1.709 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2499 ; 2.183 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1071 ; 1.347 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 873 ; 1.925 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 8 A 101 REMARK 3 RESIDUE RANGE : A 102 A 184 REMARK 3 RESIDUE RANGE : A 201 A 300 REMARK 3 ORIGIN FOR THE GROUP (A): 6.7415 69.1774 12.5990 REMARK 3 T TENSOR REMARK 3 T11: -0.0035 T22: -0.0290 REMARK 3 T33: -0.1226 T12: -0.0107 REMARK 3 T13: 0.0045 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 2.1931 L22: 0.4980 REMARK 3 L33: 0.3900 L12: -0.1493 REMARK 3 L13: -0.1451 L23: -0.1047 REMARK 3 S TENSOR REMARK 3 S11: -0.0136 S12: -0.0212 S13: -0.0045 REMARK 3 S21: -0.0190 S22: 0.0100 S23: 0.0168 REMARK 3 S31: 0.0320 S32: -0.0180 S33: 0.0036 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2BX3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1290025014. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.90 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8031 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17333 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 15.60 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 13.90 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.900 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 1UJ1 REMARK 200 REMARK 200 REMARK: DATA COLLECTED TO 1.7A BUT PROCESSED TO 2A REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG6000, 0.1M MES PH 5.9, 3% MPD, REMARK 280 PH 5.90 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 50.09850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.83750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.83750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 75.14775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.83750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.83750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.04925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.83750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.83750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 75.14775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.83750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.83750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.04925 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 50.09850 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 69.67500 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 69.67500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 50.09850 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 1 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: 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 2143 O HOH A 2257 1.93 REMARK 500 O HOH A 2191 O HOH A 2230 2.00 REMARK 500 O HOH A 2025 O HOH A 2082 2.05 REMARK 500 SG CYS A 22 NZ LYS A 61 2.09 REMARK 500 O LYS A 137 O HOH A 2139 2.09 REMARK 500 O HOH A 2144 O HOH A 2145 2.11 REMARK 500 OE2 GLU A 47 O HOH A 2059 2.14 REMARK 500 OE2 GLU A 240 O HOH A 2208 2.14 REMARK 500 OG SER A 94 O HOH A 2107 2.15 REMARK 500 OG SER A 158 O HOH A 2150 2.16 REMARK 500 O THR A 224 O HOH A 2191 2.16 REMARK 500 O HOH A 2025 O HOH A 2083 2.17 REMARK 500 O HOH A 2075 O HOH A 2161 2.18 REMARK 500 O HOH A 2166 O HOH A 2169 2.18 REMARK 500 O HOH A 2038 O HOH A 2113 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2109 O HOH A 2221 6565 1.90 REMARK 500 O HOH A 2084 O HOH A 2228 4455 2.07 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 CYS A 22 CB CYS A 22 SG -0.100 REMARK 500 CYS A 145 CB CYS A 145 SG -0.110 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 -126.21 52.51 REMARK 500 ASN A 84 -116.58 51.10 REMARK 500 ASN A 119 57.48 33.39 REMARK 500 SER A 139 44.22 -62.10 REMARK 500 ASN A 142 94.32 -29.15 REMARK 500 TYR A 154 -88.13 44.35 REMARK 500 ASN A 238 30.89 75.06 REMARK 500 ASN A 274 -24.58 -156.26 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 LYS A 137 GLY A 138 134.20 REMARK 500 GLY A 138 SER A 139 -128.55 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 A2021 DISTANCE = 8.25 ANGSTROMS REMARK 525 HOH A2022 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A2040 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A2044 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH A2048 DISTANCE = 6.59 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1O5S RELATED DB: PDB REMARK 900 STRUCTURE MODEL OF THE CATALYTIC DOMAIN OF SARS- REMARK 900 CORONAVIRUSPOLYMERASE REMARK 900 RELATED ID: 1P4X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS PROTEIN FROM STAPHYLOCOCCUS AUREUS REMARK 900 RELATED ID: 1P76 RELATED DB: PDB REMARK 900 3D STRUCTURE OF THE SUBSTRATE-BOUND SARS CHYMOTRYPSIN-LIKECYSTEINE REMARK 900 PROTEINASE REMARK 900 RELATED ID: 1P9S RELATED DB: PDB REMARK 900 CORONAVIRUS MAIN PROTEINASE (3CLPRO) STRUCTURE : BASIS FORDESIGN OF REMARK 900 ANTI-SARS DRUGS REMARK 900 RELATED ID: 1P9T RELATED DB: PDB REMARK 900 CORONAVIRUS MAIN PROTEINASE (3CLPRO) STRUCTURE : BASIS FORDESIGN OF REMARK 900 ANTI-SARS DRUGS REMARK 900 RELATED ID: 1P9U RELATED DB: PDB REMARK 900 CORONAVIRUS MAIN PROTEINASE (3CLPRO) STRUCTURE : BASIS FORDESIGN OF REMARK 900 ANTI-SARS DRUGS REMARK 900 RELATED ID: 1PA5 RELATED DB: PDB REMARK 900 STRUCTURE OF SARS CORONAVIRUS PROTEINASE REMARK 900 RELATED ID: 1PUK RELATED DB: PDB REMARK 900 3C-LIKE PROTEINASE DOMAIN STRUCTURE OF HUMAN CORONAVIRUS(STRAIN REMARK 900 SARS) MODELED IN-SILICO REMARK 900 RELATED ID: 1Q1X RELATED DB: PDB REMARK 900 CORONAVIRUS MAIN PROTEINASE (3CLPRO) STRUCTURE : BASIS FORDESIGN OF REMARK 900 ANTI-SARS LIGANDS REMARK 900 RELATED ID: 1Q2W RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF THE SARS CORONAVIRUS MAINPROTEASE REMARK 900 RELATED ID: 1Q4Z RELATED DB: PDB REMARK 900 S1 SUBUNIT MODEL OF SARS CORONAVIRUS S PROTEIN REMARK 900 RELATED ID: 1QZ8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS CORONAVIRUS NSP9 REMARK 900 RELATED ID: 1SSK RELATED DB: PDB REMARK 900 STRUCTURE OF THE N-TERMINAL RNA-BINDING DOMAIN OF THE SARSCOV REMARK 900 NUCLEOCAPSID PROTEIN REMARK 900 RELATED ID: 1SXF RELATED DB: PDB REMARK 900 HOMOLOGY MODEL FOR HUMAN SARS-CORONAVIRUS RNA-DEPENDENT REMARK 900 RNAPOLYMERASE REMARK 900 RELATED ID: 1UJ1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS CORONAVIRUS MAIN PROTEINASE(3CLPRO) REMARK 900 RELATED ID: 1UK2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS CORONAVIRUS MAIN PROTEINASE(3CLPRO) AT REMARK 900 PH8.0 REMARK 900 RELATED ID: 1UK3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS CORONAVIRUS MAIN PROTEINASE(3CLPRO) AT REMARK 900 PH7.6 REMARK 900 RELATED ID: 1UK4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS CORONAVIRUS MAIN PROTEINASE(3CLPRO) REMARK 900 COMPLEXED WITH AN INHIBITOR REMARK 900 RELATED ID: 1UW7 RELATED DB: PDB REMARK 900 NSP9 REPLICASE PROTEIN FROM SARS-CORONAVIRUS. REMARK 900 RELATED ID: 1WNC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SARS-COV SPIKE PROTEIN FUSION CORE REMARK 900 RELATED ID: 1XAK RELATED DB: PDB REMARK 900 STRUCTURE OF THE SARS-CORONAVIRUS ORF7A ACCESSORY PROTEIN REMARK 900 RELATED ID: 1XJP RELATED DB: PDB REMARK 900 MOLECULAR DOCKING MODEL OF SARS CORONAVIRUS SPIKE PROTEINS1 SUBUNIT REMARK 900 WITH ITS RECEPTOR, ACE2 REMARK 900 RELATED ID: 1XJR RELATED DB: PDB REMARK 900 THE STRUCTURE OF A RIGOROUSLY CONSERVED RNA ELEMENT WITHINTHE SARS REMARK 900 VIRUS GENOME REMARK 900 RELATED ID: 2BW6 RELATED DB: PDB REMARK 900 THE STRUCTURE OF SARS 3C LIKE PROTEASE AT 1.9A REMARK 900 RELATED ID: 2BX4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS CORONAVIRUS MAIN PROTEINASE (P21212) DBREF 2BX3 A 1 306 UNP P0C6U8 R1A_SARS 3241 3546 SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP THR VAL TYR CYS PRO SEQRES 4 A 306 ARG HIS VAL ILE CYS THR ALA GLU ASP MET LEU ASN PRO SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS SER SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS LEU LEU ARG LEU LYS VAL SEQRES 8 A 306 ASP THR SER ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 A 306 ARG PRO ASN HIS THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY LYS PHE TYR SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 A 306 THR ASP THR THR ILE THR LEU ASN VAL LEU ALA TRP LEU SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 A 306 VAL LEU ASP MET CYS ALA ALA LEU LYS GLU LEU LEU GLN SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER THR ILE SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN FORMUL 2 HOH *259(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 GLU A 47 ASN A 51 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 ASN A 214 1 15 HELIX 7 7 THR A 226 TYR A 237 1 12 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 SER A 301 1 10 SHEET 1 AA 7 VAL A 73 LEU A 75 0 SHEET 2 AA 7 PHE A 66 ALA A 70 -1 O VAL A 68 N LEU A 75 SHEET 3 AA 7 MET A 17 CYS A 22 -1 O GLN A 19 N GLN A 69 SHEET 4 AA 7 THR A 25 LEU A 32 -1 O THR A 25 N CYS A 22 SHEET 5 AA 7 THR A 35 PRO A 39 -1 O THR A 35 N LEU A 32 SHEET 6 AA 7 LEU A 86 VAL A 91 -1 O LEU A 87 N CYS A 38 SHEET 7 AA 7 VAL A 77 GLN A 83 -1 N ILE A 78 O LYS A 90 SHEET 1 AB 5 TYR A 101 PHE A 103 0 SHEET 2 AB 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 102 SHEET 3 AB 5 VAL A 148 ASP A 153 -1 O GLY A 149 N CYS A 160 SHEET 4 AB 5 THR A 111 TYR A 118 -1 O SER A 113 N PHE A 150 SHEET 5 AB 5 SER A 121 ALA A 129 -1 O SER A 121 N TYR A 118 SHEET 1 AC 3 TYR A 101 PHE A 103 0 SHEET 2 AC 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 102 SHEET 3 AC 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 CRYST1 69.675 69.675 100.197 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 0.014352 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009980 0.00000