PDB Short entry for 7MHP HEADER HYDROLASE 15-APR-21 7MHP TITLE ENSEMBLE REFINEMENT STRUCTURE OF SARS-COV-2 MAIN PROTEASE (MPRO) AT TITLE 2 298 K AT HIGH HUMIDITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3CL-PRO,3CLP,MAIN PROTEASE,MPRO,NON-STRUCTURAL PROTEIN 5, COMPND 5 NSP5,SARS CORONAVIRUS MAIN PROTEINASE; COMPND 6 EC: 3.4.22.69; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: REP, 1A-1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET29B KEYWDS SARS-COV-2, CORONAVIRUS, MAIN PROTEASE, 3CLPRO, MPRO, HYDROLASE, KEYWDS 2 ENSEMBLE REFINEMENT, TEMPERATURE SERIES, TEMPERATURE, KEYWDS 3 MULTITEMPERATURE, HUMIDITY EXPDTA X-RAY DIFFRACTION NUMMDL 28 AUTHOR A.EBRAHIM,B.T.RILEY,D.KUMARAN,B.ANDI,M.R.FUCHS,S.MCSWEENEY,D.A.KEEDY REVDAT 5 18-OCT-23 7MHP 1 REMARK REVDAT 4 07-SEP-22 7MHP 1 JRNL REVDAT 3 06-APR-22 7MHP 1 TITLE COMPND SOURCE KEYWDS REVDAT 3 2 1 JRNL REMARK HET HETNAM REVDAT 3 3 1 FORMUL HELIX SHEET LINK REVDAT 3 4 1 ATOM REVDAT 2 26-MAY-21 7MHP 1 JRNL REVDAT 1 12-MAY-21 7MHP 0 JRNL AUTH A.EBRAHIM,B.T.RILEY,D.KUMARAN,B.ANDI,M.R.FUCHS,S.MCSWEENEY, JRNL AUTH 2 D.A.KEEDY JRNL TITL THE TEMPERATURE-DEPENDENT CONFORMATIONAL ENSEMBLE OF JRNL TITL 2 SARS-COV-2 MAIN PROTEASE (M PRO ) JRNL REF IUCRJ V. 9 682 2022 JRNL REFN ESSN 2052-2525 JRNL DOI 10.1107/S2052252522007497 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.ENSEMBLE_REFINEMENT:1.19.2_4158) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 18575 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 56.3000 - 3.8300 1.00 2583 168 0.1170 0.1587 REMARK 3 2 3.8300 - 3.0400 1.00 2536 116 0.1493 0.2244 REMARK 3 3 3.0400 - 2.6500 0.99 2524 118 0.1928 0.3328 REMARK 3 4 2.6500 - 2.4100 0.99 2527 135 0.1902 0.3173 REMARK 3 5 2.4100 - 2.2400 0.99 2496 135 0.2229 0.2980 REMARK 3 6 2.2400 - 2.1100 0.99 2488 126 0.2375 0.3253 REMARK 3 7 2.1100 - 2.0005 0.98 2497 126 0.2748 0.3320 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7MHP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000255383. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 0.7.32-G2F242514-DIALS-3.0 REMARK 200 DATA SCALING SOFTWARE : DIALS 3.0.0-GB83E1FCE8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18588 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.001 REMARK 200 RESOLUTION RANGE LOW (A) : 56.303 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.772 REMARK 200 R MERGE (I) : 0.17810 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.2709 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) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.67 REMARK 200 R MERGE FOR SHELL (I) : 1.70850 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.553 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.18.2_3874 REMARK 200 STARTING MODEL: 6YB7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 4000, 100 MM HEPES PH 7.0, 3- REMARK 280 -5% DMSO, VAPOR DIFFUSION, 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 57.44000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.36800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.44000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.36800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 512 LIES ON A SPECIAL POSITION. 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 1 CYS A 128 CB CYS A 128 SG -0.113 REMARK 500 1 CYS A 156 CB CYS A 156 SG 0.117 REMARK 500 1 GLU A 288 CB GLU A 288 CG 0.125 REMARK 500 2 CYS A 145 CB CYS A 145 SG 0.109 REMARK 500 3 CYS A 300 CB CYS A 300 SG 0.110 REMARK 500 4 CYS A 156 CB CYS A 156 SG -0.210 REMARK 500 5 CYS A 16 CB CYS A 16 SG -0.133 REMARK 500 5 GLU A 178 CB GLU A 178 CG 0.164 REMARK 500 6 CYS A 128 CB CYS A 128 SG -0.102 REMARK 500 7 CYS A 128 CB CYS A 128 SG -0.102 REMARK 500 10 CYS A 145 CB CYS A 145 SG -0.106 REMARK 500 10 MET A 165 CB MET A 165 CG 0.215 REMARK 500 10 CYS A 300 CB CYS A 300 SG 0.237 REMARK 500 11 CYS A 16 CB CYS A 16 SG -0.110 REMARK 500 11 CYS A 300 CB CYS A 300 SG 0.120 REMARK 500 12 CYS A 44 CB CYS A 44 SG -0.108 REMARK 500 12 CYS A 128 CB CYS A 128 SG -0.107 REMARK 500 13 CYS A 16 CB CYS A 16 SG -0.099 REMARK 500 14 CYS A 145 CB CYS A 145 SG 0.145 REMARK 500 16 CYS A 145 CB CYS A 145 SG 0.136 REMARK 500 17 CYS A 156 CB CYS A 156 SG 0.175 REMARK 500 18 CYS A 300 CB CYS A 300 SG 0.167 REMARK 500 21 CYS A 16 CB CYS A 16 SG -0.098 REMARK 500 21 CYS A 145 CB CYS A 145 SG 0.221 REMARK 500 24 CYS A 22 CB CYS A 22 SG -0.104 REMARK 500 25 CYS A 145 CB CYS A 145 SG -0.157 REMARK 500 25 CYS A 300 CB CYS A 300 SG -0.100 REMARK 500 26 CYS A 128 CB CYS A 128 SG -0.122 REMARK 500 26 CYS A 145 CB CYS A 145 SG -0.179 REMARK 500 26 CYS A 265 CB CYS A 265 SG -0.108 REMARK 500 27 CYS A 156 CB CYS A 156 SG -0.134 REMARK 500 28 GLU A 288 CB GLU A 288 CG 0.175 REMARK 500 28 GLU A 288 CG GLU A 288 CD 0.091 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 3 MET A 6 CG - SD - CE ANGL. DEV. = -9.8 DEGREES REMARK 500 4 CYS A 156 CA - CB - SG ANGL. DEV. = 8.8 DEGREES REMARK 500 5 LEU A 67 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 7 CYS A 156 CA - CB - SG ANGL. DEV. = 11.4 DEGREES REMARK 500 9 MET A 235 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 10 LEU A 141 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 10 LEU A 242 CA - CB - CG ANGL. DEV. = 15.5 DEGREES REMARK 500 10 CYS A 300 CA - CB - SG ANGL. DEV. = 8.6 DEGREES REMARK 500 11 MET A 276 CA - CB - CG ANGL. DEV. = 10.8 DEGREES REMARK 500 12 ASP A 155 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 13 CYS A 145 CA - CB - SG ANGL. DEV. = -12.6 DEGREES REMARK 500 13 LEU A 272 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 17 ASP A 289 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 18 ASP A 197 CB - CG - OD1 ANGL. DEV. = -6.3 DEGREES REMARK 500 18 LEU A 242 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 18 CYS A 300 CA - CB - SG ANGL. DEV. = 10.8 DEGREES REMARK 500 19 LEU A 167 CA - CB - CG ANGL. DEV. = 16.4 DEGREES REMARK 500 21 CYS A 145 CA - CB - SG ANGL. DEV. = 14.7 DEGREES REMARK 500 24 ASP A 153 CB - CG - OD1 ANGL. DEV. = 8.0 DEGREES REMARK 500 25 LEU A 286 CA - CB - CG ANGL. DEV. = 16.8 DEGREES REMARK 500 25 VAL A 303 CA - CB - CG1 ANGL. DEV. = 11.5 DEGREES REMARK 500 26 CYS A 145 CA - CB - SG ANGL. DEV. = -11.2 DEGREES REMARK 500 26 LEU A 286 CA - CB - CG ANGL. DEV. = 16.3 DEGREES REMARK 500 27 LEU A 67 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 27 CYS A 156 CA - CB - SG ANGL. DEV. = 8.0 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 1 THR A 24 -86.68 -75.66 REMARK 500 1 THR A 25 159.30 -23.94 REMARK 500 1 ASP A 33 -110.04 41.53 REMARK 500 1 SER A 46 -84.65 66.28 REMARK 500 1 MET A 49 -41.16 -25.48 REMARK 500 1 ASN A 51 55.47 -168.52 REMARK 500 1 SER A 62 115.12 -35.50 REMARK 500 1 ASN A 63 -152.33 -41.02 REMARK 500 1 HIS A 64 50.03 28.34 REMARK 500 1 ASN A 65 -68.81 -164.42 REMARK 500 1 PHE A 66 113.85 -27.50 REMARK 500 1 ALA A 70 78.42 -178.19 REMARK 500 1 ASN A 84 -117.17 44.16 REMARK 500 1 LYS A 90 67.27 -106.22 REMARK 500 1 VAL A 91 -179.08 -66.14 REMARK 500 1 ASP A 155 42.00 38.05 REMARK 500 1 CYS A 156 -150.05 71.46 REMARK 500 1 HIS A 164 -60.97 -121.98 REMARK 500 1 PRO A 184 30.57 -85.07 REMARK 500 1 ALA A 191 128.57 -39.81 REMARK 500 1 GLN A 192 -148.75 -133.05 REMARK 500 1 ALA A 193 94.93 168.71 REMARK 500 1 PHE A 223 -168.86 -118.99 REMARK 500 1 THR A 224 -167.23 176.47 REMARK 500 1 THR A 225 176.72 174.98 REMARK 500 1 ASN A 274 100.70 150.12 REMARK 500 1 MET A 276 -130.17 -45.76 REMARK 500 1 THR A 280 151.55 59.03 REMARK 500 1 ARG A 298 -77.14 -40.76 REMARK 500 1 GLN A 299 176.01 -56.56 REMARK 500 1 CYS A 300 -35.25 61.71 REMARK 500 1 SER A 301 -103.86 -147.52 REMARK 500 1 THR A 304 -89.64 -124.06 REMARK 500 2 THR A 25 131.82 51.08 REMARK 500 2 ASP A 33 -122.79 22.47 REMARK 500 2 HIS A 41 -3.35 -53.43 REMARK 500 2 ASN A 51 67.11 -176.49 REMARK 500 2 ASN A 63 -83.30 3.04 REMARK 500 2 HIS A 64 45.92 -59.62 REMARK 500 2 ASN A 65 -60.08 -149.18 REMARK 500 2 PHE A 66 119.48 -19.66 REMARK 500 2 ILE A 78 65.93 -109.75 REMARK 500 2 ASN A 84 -122.54 43.97 REMARK 500 2 LYS A 100 96.85 -42.15 REMARK 500 2 ILE A 152 -135.50 -114.79 REMARK 500 2 ASP A 153 -100.66 117.80 REMARK 500 2 TYR A 154 162.96 174.35 REMARK 500 2 ASP A 155 -6.48 37.67 REMARK 500 2 CYS A 156 -159.84 109.58 REMARK 500 2 PRO A 168 -34.86 -20.97 REMARK 500 REMARK 500 THIS ENTRY HAS 826 RAMACHANDRAN OUTLIERS. 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 GLY A 23 THR A 24 1 142.65 REMARK 500 THR A 24 THR A 25 1 -147.72 REMARK 500 SER A 62 ASN A 63 1 142.24 REMARK 500 ASN A 63 HIS A 64 1 149.29 REMARK 500 GLY A 79 HIS A 80 1 -134.06 REMARK 500 ASP A 155 CYS A 156 1 149.12 REMARK 500 CYS A 156 VAL A 157 1 -125.45 REMARK 500 MET A 276 ASN A 277 1 137.18 REMARK 500 VAL A 303 THR A 304 1 146.03 REMARK 500 SER A 62 ASN A 63 2 145.73 REMARK 500 ILE A 152 ASP A 153 2 -144.05 REMARK 500 ASP A 155 CYS A 156 2 105.91 REMARK 500 LEU A 242 THR A 243 2 147.73 REMARK 500 GLY A 275 MET A 276 2 148.54 REMARK 500 ARG A 279 THR A 280 2 -140.69 REMARK 500 VAL A 303 THR A 304 2 -142.91 REMARK 500 GLY A 23 THR A 24 3 142.21 REMARK 500 LEU A 75 ARG A 76 3 139.58 REMARK 500 ASP A 153 TYR A 154 3 127.84 REMARK 500 CYS A 156 VAL A 157 3 -126.70 REMARK 500 VAL A 171 HIS A 172 3 -148.34 REMARK 500 LEU A 242 THR A 243 3 139.19 REMARK 500 THR A 304 PHE A 305 3 145.53 REMARK 500 ASP A 153 TYR A 154 4 132.24 REMARK 500 MET A 276 ASN A 277 4 119.04 REMARK 500 SER A 301 GLY A 302 4 -149.49 REMARK 500 THR A 45 SER A 46 5 148.06 REMARK 500 ASN A 72 VAL A 73 5 147.73 REMARK 500 GLY A 143 SER A 144 5 -142.58 REMARK 500 ASN A 221 ARG A 222 5 147.36 REMARK 500 PHE A 223 THR A 224 5 -143.16 REMARK 500 MET A 276 ASN A 277 5 139.48 REMARK 500 ARG A 279 THR A 280 5 144.81 REMARK 500 ASN A 151 ILE A 152 6 144.08 REMARK 500 ASP A 155 CYS A 156 6 -131.70 REMARK 500 ARG A 222 PHE A 223 6 -131.51 REMARK 500 ARG A 279 THR A 280 6 123.74 REMARK 500 TYR A 154 ASP A 155 7 -142.33 REMARK 500 ASN A 274 GLY A 275 7 134.34 REMARK 500 CYS A 300 SER A 301 7 149.32 REMARK 500 GLY A 302 VAL A 303 7 127.08 REMARK 500 THR A 304 PHE A 305 7 -144.07 REMARK 500 ASN A 151 ILE A 152 8 134.82 REMARK 500 TYR A 154 ASP A 155 8 -148.77 REMARK 500 ASP A 155 CYS A 156 8 149.35 REMARK 500 CYS A 156 VAL A 157 8 134.89 REMARK 500 ASN A 221 ARG A 222 8 -131.63 REMARK 500 LEU A 227 ASN A 228 8 -148.59 REMARK 500 THR A 304 PHE A 305 8 -118.70 REMARK 500 GLU A 47 ASP A 48 9 -148.24 REMARK 500 REMARK 500 THIS ENTRY HAS 181 NON CIS, NON-TRANS OMEGA OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 188 0.08 SIDE CHAIN REMARK 500 1 ARG A 279 0.07 SIDE CHAIN REMARK 500 2 ARG A 298 0.12 SIDE CHAIN REMARK 500 4 ARG A 298 0.09 SIDE CHAIN REMARK 500 8 ARG A 217 0.10 SIDE CHAIN REMARK 500 11 ARG A 76 0.09 SIDE CHAIN REMARK 500 11 ARG A 298 0.23 SIDE CHAIN REMARK 500 13 ARG A 105 0.08 SIDE CHAIN REMARK 500 13 ARG A 298 0.08 SIDE CHAIN REMARK 500 17 ARG A 298 0.10 SIDE CHAIN REMARK 500 18 ARG A 279 0.09 SIDE CHAIN REMARK 500 19 ARG A 298 0.08 SIDE CHAIN 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 41 NE2 REMARK 620 2 CYS A 145 SG 106.9 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7MHL RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT AT 100 K REMARK 900 RELATED ID: 7MHM RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT AT 240 K REMARK 900 RELATED ID: 7MHN RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT AT 277 K REMARK 900 RELATED ID: 7MHO RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT AT 298 K REMARK 900 RELATED ID: 7MHQ RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT AT 310 K REMARK 900 RELATED ID: 7MHF RELATED DB: PDB REMARK 900 REFINEMENT AT 100 K REMARK 900 RELATED ID: 7MHG RELATED DB: PDB REMARK 900 REFINEMENT AT 240 K REMARK 900 RELATED ID: 7MHH RELATED DB: PDB REMARK 900 REFINEMENT AT 277 K REMARK 900 RELATED ID: 7MHI RELATED DB: PDB REMARK 900 REFINEMENT AT 298 K REMARK 900 RELATED ID: 7MHJ RELATED DB: PDB REMARK 900 REFINEMENT AT 298 K, 99% RH REMARK 900 RELATED ID: 7MHK RELATED DB: PDB REMARK 900 REFINEMENT AT 310 K DBREF 7MHP A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 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 VAL VAL TYR CYS PRO SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN 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 VAL LEU LYS LEU LYS VAL SEQRES 8 A 306 ASP THR ALA 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 PHE 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 ASN 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 VAL 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 SER LEU LYS GLU LEU LEU GLN SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU 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 HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *34(H2 O) HELIX 1 AA1 SER A 10 GLY A 15 1 6 HELIX 2 AA2 HIS A 41 CYS A 44 5 4 HELIX 3 AA3 ASN A 53 ARG A 60 1 8 HELIX 4 AA4 ILE A 200 ASN A 214 1 15 HELIX 5 AA5 ASN A 228 MET A 235 1 8 HELIX 6 AA6 THR A 243 GLY A 258 1 16 HELIX 7 AA7 ALA A 260 ASN A 274 1 15 HELIX 8 AA8 THR A 292 GLN A 299 1 8 SHEET 1 AA1 7 VAL A 73 ARG A 76 0 SHEET 2 AA1 7 LEU A 67 ALA A 70 -1 N VAL A 68 O LEU A 75 SHEET 3 AA1 7 MET A 17 THR A 21 -1 N THR A 21 O LEU A 67 SHEET 4 AA1 7 THR A 26 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O VAL A 35 N LEU A 32 SHEET 6 AA1 7 VAL A 86 LEU A 89 -1 O LEU A 87 N CYS A 38 SHEET 7 AA1 7 HIS A 80 GLN A 83 -1 N GLN A 83 O VAL A 86 SHEET 1 AA2 5 TYR A 101 PHE A 103 0 SHEET 2 AA2 5 VAL A 157 GLU A 166 1 O VAL A 157 N LYS A 102 SHEET 3 AA2 5 VAL A 148 ASN A 151 -1 N GLY A 149 O CYS A 160 SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 121 N TYR A 118 SHEET 1 AA3 3 TYR A 101 PHE A 103 0 SHEET 2 AA3 3 VAL A 157 GLU A 166 1 O VAL A 157 N LYS A 102 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 LINK NE2 HIS A 41 ZN ZN A 401 1555 1555 2.51 LINK SG CYS A 145 ZN ZN A 401 1555 1555 2.35 CRYST1 114.880 54.736 45.240 90.00 101.42 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008705 0.000000 0.001758 0.00000 SCALE2 0.000000 0.018270 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022551 0.00000