HEADER VIRAL PROTEIN 20-NOV-20 7KS5 OBSLTE 03-FEB-21 7KS5 7LFE TITLE SARS-COV-2 MAIN PROTEASE IMMATURE FORM - F2X ENTRY LIBRARY E03 TITLE 2 FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3CL-PRO,3CLP,MAIN PROTEASE,MPRO,NON-STRUCTURAL PROTEIN 5, COMPND 5 NSP5,SARS CORONAVIRUS MAIN PROTEINASE,REPLICASE POLYPROTEIN 1AB; 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_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MPRO, SARS-COV-2, COVID-19, PROTEASE, VIRAL PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.D.NOSKE,A.M.NAKAMURA,V.O.GAWRILJUK,G.M.A.LIMA,A.C.M.ZERI, AUTHOR 2 A.F.Z.NASCIMENTO,G.OLIVA,A.S.GODOY REVDAT 3 03-FEB-21 7KS5 1 OBSLTE REVDAT 2 27-JAN-21 7KS5 1 COMPND REVDAT 1 09-DEC-20 7KS5 0 JRNL AUTH G.D.NOSKE,A.M.NAKAMURA,V.O.GAWRILJUK,G.M.A.LIMA,A.C.M.ZERI, JRNL AUTH 2 A.F.Z.NASCIMENTO,G.OLIVA,A.S.GODOY JRNL TITL SARS-COV-2 MAIN PROTEASE IN MATURE FORM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 16723 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1678 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 56.4600 - 6.4400 1.00 1440 163 0.1976 0.2144 REMARK 3 2 6.4400 - 5.1100 1.00 1367 150 0.2089 0.2257 REMARK 3 3 5.1100 - 4.4700 1.00 1353 153 0.1724 0.1960 REMARK 3 4 4.4700 - 4.0600 1.00 1336 149 0.1729 0.2184 REMARK 3 5 4.0600 - 3.7700 0.82 1085 124 0.2140 0.2272 REMARK 3 6 3.7700 - 3.5500 0.82 1077 117 0.2619 0.3553 REMARK 3 7 3.5500 - 3.3700 0.61 815 93 0.2335 0.2794 REMARK 3 8 3.3700 - 3.2200 1.00 1309 147 0.2292 0.2818 REMARK 3 9 3.2200 - 3.1000 1.00 1318 148 0.2435 0.3190 REMARK 3 10 3.1000 - 2.9900 1.00 1326 145 0.2398 0.2911 REMARK 3 11 2.9900 - 2.9000 1.00 1316 145 0.2605 0.2813 REMARK 3 12 2.9000 - 2.8100 1.00 1303 144 0.2878 0.3389 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.482 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.71 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 : 0.008 4837 REMARK 3 ANGLE : 1.725 6555 REMARK 3 CHIRALITY : 0.090 732 REMARK 3 PLANARITY : 0.009 846 REMARK 3 DIHEDRAL : 15.610 689 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -2.1101 -3.2746 16.4885 REMARK 3 T TENSOR REMARK 3 T11: 0.2639 T22: 0.2360 REMARK 3 T33: 0.2933 T12: 0.0079 REMARK 3 T13: 0.0013 T23: -0.0402 REMARK 3 L TENSOR REMARK 3 L11: 0.8930 L22: 0.5733 REMARK 3 L33: 1.4877 L12: 0.4041 REMARK 3 L13: -0.2309 L23: -0.2685 REMARK 3 S TENSOR REMARK 3 S11: -0.0085 S12: -0.0278 S13: 0.0438 REMARK 3 S21: -0.0581 S22: -0.0419 S23: -0.0512 REMARK 3 S31: 0.0976 S32: -0.0152 S33: 0.0275 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 2 through 157 or REMARK 3 resid 159 through 301 or resid 601)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 2 through 157 or REMARK 3 resid 159 through 301 or resid 501)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7KS5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000253096. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS SIRUS REMARK 200 BEAMLINE : MANACA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.35502 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16800 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.810 REMARK 200 RESOLUTION RANGE LOW (A) : 56.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.19700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.95000 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: PHASER REMARK 200 STARTING MODEL: 7KFI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.7, 5% DMSO, 8% PEG REMARK 280 4000, VAPOR DIFFUSION, TEMPERATURE 293K 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 33.89250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.33350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.33350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.89250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.00000 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: 4610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 REMARK 465 GLN A 306 REMARK 465 GLY B -2 REMARK 465 ALA B -1 REMARK 465 MET B 0 REMARK 465 SER B 1 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 OH TYR B 118 O PHE B 140 2.04 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 OD1 ASP A 33 NE2 HIS B 64 4445 2.03 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 GLU A 166 CB GLU A 166 CG -0.181 REMARK 500 GLU A 166 CG GLU A 166 CD -0.122 REMARK 500 LYS B 102 CD LYS B 102 CE 0.156 REMARK 500 PHE B 294 CB PHE B 294 CG -0.128 REMARK 500 ARG B 298 CZ ARG B 298 NH2 -0.081 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 TYR A 154 CB - CG - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 GLU A 166 OE1 - CD - OE2 ANGL. DEV. = -52.3 DEGREES REMARK 500 GLU A 166 CG - CD - OE1 ANGL. DEV. = 29.1 DEGREES REMARK 500 GLU A 166 CG - CD - OE2 ANGL. DEV. = -41.2 DEGREES REMARK 500 LEU A 232 CB - CG - CD1 ANGL. DEV. = 22.6 DEGREES REMARK 500 LEU A 232 CB - CG - CD2 ANGL. DEV. = -34.9 DEGREES REMARK 500 LEU B 50 CB - CG - CD2 ANGL. DEV. = 11.3 DEGREES REMARK 500 ASN B 51 N - CA - CB ANGL. DEV. = -13.4 DEGREES REMARK 500 ARG B 217 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG B 217 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 PHE B 294 CB - CG - CD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG B 298 CA - CB - CG ANGL. DEV. = -21.1 DEGREES REMARK 500 ARG B 298 CB - CG - CD ANGL. DEV. = 23.0 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 ASP A 33 -130.34 57.85 REMARK 500 ASN A 51 58.50 -150.56 REMARK 500 ASN A 84 -123.08 57.81 REMARK 500 PHE A 140 15.63 -67.92 REMARK 500 ASN A 142 -73.25 -88.11 REMARK 500 ASP A 155 7.45 58.51 REMARK 500 ALA A 191 108.08 -58.70 REMARK 500 ASP B 33 -128.91 56.26 REMARK 500 SER B 46 10.24 -54.76 REMARK 500 GLU B 47 -47.43 -155.55 REMARK 500 ASN B 51 36.87 -162.02 REMARK 500 ASN B 84 -121.76 56.20 REMARK 500 ASN B 277 64.90 36.40 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 SER B 46 GLU B 47 -123.56 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 TYR A 154 0.07 SIDE CHAIN REMARK 500 GLN B 69 0.07 SIDE CHAIN REMARK 500 PHE B 294 0.09 SIDE CHAIN REMARK 500 ARG B 298 0.08 SIDE CHAIN 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 628 DISTANCE = 6.93 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue X1Y A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 703 DBREF 7KS5 A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 7KS5 B 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQADV 7KS5 GLY A -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7KS5 ALA A -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7KS5 MET A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7KS5 GLY B -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7KS5 ALA B -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7KS5 MET B 0 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 309 GLY ALA MET SER GLY PHE ARG LYS MET ALA PHE PRO SER SEQRES 2 A 309 GLY LYS VAL GLU GLY CYS MET VAL GLN VAL THR CYS GLY SEQRES 3 A 309 THR THR THR LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL SEQRES 4 A 309 TYR CYS PRO ARG HIS VAL ILE CYS THR SER GLU ASP MET SEQRES 5 A 309 LEU ASN PRO ASN TYR GLU ASP LEU LEU ILE ARG LYS SER SEQRES 6 A 309 ASN HIS ASN PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU SEQRES 7 A 309 ARG VAL ILE GLY HIS SER MET GLN ASN CYS VAL LEU LYS SEQRES 8 A 309 LEU LYS VAL ASP THR ALA ASN PRO LYS THR PRO LYS TYR SEQRES 9 A 309 LYS PHE VAL ARG ILE GLN PRO GLY GLN THR PHE SER VAL SEQRES 10 A 309 LEU ALA CYS TYR ASN GLY SER PRO SER GLY VAL TYR GLN SEQRES 11 A 309 CYS ALA MET ARG PRO ASN PHE THR ILE LYS GLY SER PHE SEQRES 12 A 309 LEU ASN GLY SER CYS GLY SER VAL GLY PHE ASN ILE ASP SEQRES 13 A 309 TYR ASP CYS VAL SER PHE CYS TYR MET HIS HIS MET GLU SEQRES 14 A 309 LEU PRO THR GLY VAL HIS ALA GLY THR ASP LEU GLU GLY SEQRES 15 A 309 ASN PHE TYR GLY PRO PHE VAL ASP ARG GLN THR ALA GLN SEQRES 16 A 309 ALA ALA GLY THR ASP THR THR ILE THR VAL ASN VAL LEU SEQRES 17 A 309 ALA TRP LEU TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP SEQRES 18 A 309 PHE LEU ASN ARG PHE THR THR THR LEU ASN ASP PHE ASN SEQRES 19 A 309 LEU VAL ALA MET LYS TYR ASN TYR GLU PRO LEU THR GLN SEQRES 20 A 309 ASP HIS VAL ASP ILE LEU GLY PRO LEU SER ALA GLN THR SEQRES 21 A 309 GLY ILE ALA VAL LEU ASP MET CYS ALA SER LEU LYS GLU SEQRES 22 A 309 LEU LEU GLN ASN GLY MET ASN GLY ARG THR ILE LEU GLY SEQRES 23 A 309 SER ALA LEU LEU GLU ASP GLU PHE THR PRO PHE ASP VAL SEQRES 24 A 309 VAL ARG GLN CYS SER GLY VAL THR PHE GLN SEQRES 1 B 309 GLY ALA MET SER GLY PHE ARG LYS MET ALA PHE PRO SER SEQRES 2 B 309 GLY LYS VAL GLU GLY CYS MET VAL GLN VAL THR CYS GLY SEQRES 3 B 309 THR THR THR LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL SEQRES 4 B 309 TYR CYS PRO ARG HIS VAL ILE CYS THR SER GLU ASP MET SEQRES 5 B 309 LEU ASN PRO ASN TYR GLU ASP LEU LEU ILE ARG LYS SER SEQRES 6 B 309 ASN HIS ASN PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU SEQRES 7 B 309 ARG VAL ILE GLY HIS SER MET GLN ASN CYS VAL LEU LYS SEQRES 8 B 309 LEU LYS VAL ASP THR ALA ASN PRO LYS THR PRO LYS TYR SEQRES 9 B 309 LYS PHE VAL ARG ILE GLN PRO GLY GLN THR PHE SER VAL SEQRES 10 B 309 LEU ALA CYS TYR ASN GLY SER PRO SER GLY VAL TYR GLN SEQRES 11 B 309 CYS ALA MET ARG PRO ASN PHE THR ILE LYS GLY SER PHE SEQRES 12 B 309 LEU ASN GLY SER CYS GLY SER VAL GLY PHE ASN ILE ASP SEQRES 13 B 309 TYR ASP CYS VAL SER PHE CYS TYR MET HIS HIS MET GLU SEQRES 14 B 309 LEU PRO THR GLY VAL HIS ALA GLY THR ASP LEU GLU GLY SEQRES 15 B 309 ASN PHE TYR GLY PRO PHE VAL ASP ARG GLN THR ALA GLN SEQRES 16 B 309 ALA ALA GLY THR ASP THR THR ILE THR VAL ASN VAL LEU SEQRES 17 B 309 ALA TRP LEU TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP SEQRES 18 B 309 PHE LEU ASN ARG PHE THR THR THR LEU ASN ASP PHE ASN SEQRES 19 B 309 LEU VAL ALA MET LYS TYR ASN TYR GLU PRO LEU THR GLN SEQRES 20 B 309 ASP HIS VAL ASP ILE LEU GLY PRO LEU SER ALA GLN THR SEQRES 21 B 309 GLY ILE ALA VAL LEU ASP MET CYS ALA SER LEU LYS GLU SEQRES 22 B 309 LEU LEU GLN ASN GLY MET ASN GLY ARG THR ILE LEU GLY SEQRES 23 B 309 SER ALA LEU LEU GLU ASP GLU PHE THR PRO PHE ASP VAL SEQRES 24 B 309 VAL ARG GLN CYS SER GLY VAL THR PHE GLN HET PEG A 501 7 HET PEG A 502 7 HET X1Y A 503 14 HET DMS A 504 4 HET DMS A 505 4 HET DMS A 506 4 HET DMS A 507 4 HET DMS A 508 4 HET PEG B 701 7 HET DMS B 702 4 HET PEG B 703 7 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM X1Y (2R,4R)-1-CYCLOHEXYLHEXAHYDROPYRIMIDINE-2,4-DIOL HETNAM DMS DIMETHYL SULFOXIDE FORMUL 3 PEG 4(C4 H10 O3) FORMUL 5 X1Y C10 H20 N2 O2 FORMUL 6 DMS 6(C2 H6 O S) FORMUL 14 HOH *42(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 GLU A 47 ASN A 51 5 5 HELIX 4 AA4 ASN A 53 ARG A 60 1 8 HELIX 5 AA5 SER A 62 HIS A 64 5 3 HELIX 6 AA6 ILE A 200 ASN A 214 1 15 HELIX 7 AA7 THR A 226 MET A 235 1 10 HELIX 8 AA8 LYS A 236 ASN A 238 5 3 HELIX 9 AA9 THR A 243 LEU A 250 1 8 HELIX 10 AB1 LEU A 250 GLY A 258 1 9 HELIX 11 AB2 ALA A 260 GLY A 275 1 16 HELIX 12 AB3 THR A 292 CYS A 300 1 9 HELIX 13 AB4 SER B 10 GLY B 15 1 6 HELIX 14 AB5 HIS B 41 CYS B 44 5 4 HELIX 15 AB6 ASN B 53 ARG B 60 1 8 HELIX 16 AB7 SER B 62 HIS B 64 5 3 HELIX 17 AB8 SER B 139 GLY B 143 5 5 HELIX 18 AB9 ILE B 200 ASN B 214 1 15 HELIX 19 AC1 THR B 226 TYR B 237 1 12 HELIX 20 AC2 THR B 243 LEU B 250 1 8 HELIX 21 AC3 LEU B 250 GLY B 258 1 9 HELIX 22 AC4 ALA B 260 GLY B 275 1 16 HELIX 23 AC5 THR B 292 SER B 301 1 10 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N VAL A 68 O LEU A 75 SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67 SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30 SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36 SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N SER A 81 O LYS A 88 SHEET 1 AA2 5 LYS A 100 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158 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 123 N ALA A 116 SHEET 1 AA3 3 LYS A 100 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N HIS A 164 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 PHE B 66 ALA B 70 -1 N ALA B 70 O VAL B 73 SHEET 3 AA4 7 MET B 17 CYS B 22 -1 N GLN B 19 O GLN B 69 SHEET 4 AA4 7 THR B 25 LEU B 32 -1 O GLY B 29 N VAL B 18 SHEET 5 AA4 7 VAL B 35 PRO B 39 -1 O TYR B 37 N LEU B 30 SHEET 6 AA4 7 VAL B 86 VAL B 91 -1 O LEU B 87 N CYS B 38 SHEET 7 AA4 7 VAL B 77 GLN B 83 -1 N ILE B 78 O LYS B 90 SHEET 1 AA5 5 TYR B 101 PHE B 103 0 SHEET 2 AA5 5 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA5 5 VAL B 148 ASP B 153 -1 N ASN B 151 O SER B 158 SHEET 4 AA5 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150 SHEET 5 AA5 5 SER B 121 ALA B 129 -1 O SER B 123 N ALA B 116 SHEET 1 AA6 4 TYR B 101 PHE B 103 0 SHEET 2 AA6 4 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA6 4 VAL B 171 THR B 175 -1 O ALA B 173 N MET B 165 SHEET 4 AA6 4 ILE B 136 LYS B 137 -1 N ILE B 136 O HIS B 172 SITE 1 AC1 4 GLY B 79 HIS B 80 SER B 81 LYS B 90 SITE 1 AC2 2 GLN A 19 LEU A 67 SITE 1 AC3 5 HIS A 41 CYS A 145 MET A 165 GLU A 166 SITE 2 AC3 5 GLN A 189 SITE 1 AC4 3 SER A 123 MET B 6 GLN B 127 SITE 1 AC5 2 ARG A 40 ASN A 84 SITE 1 AC6 5 GLN A 19 GLN A 69 GLY A 71 ASN A 119 SITE 2 AC6 5 GLY A 120 SITE 1 AC7 4 LEU A 272 GLY A 275 MET A 276 LEU A 287 SITE 1 AC8 3 MET A 6 PHE A 8 SER B 123 SITE 1 AC9 3 GLU A 290 PHE B 3 ARG B 4 SITE 1 AD1 1 GLN B 127 SITE 1 AD2 2 GLY B 15 LYS B 97 CRYST1 67.785 102.000 102.667 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 0.014753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009804 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009740 0.00000