HEADER VIRAL PROTEIN 28-JUN-21 7OZU TITLE SARS-COV-2 RDRP WITH MOLNUPIRAVIR/ NHC IN THE TEMPLATE STRAND BASE- TITLE 2 PAIRED WITH A COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICASE POLYPROTEIN 1AB; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PP1AB,ORF1AB POLYPROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NON-STRUCTURAL PROTEIN 8; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: NSP8; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: NON-STRUCTURAL PROTEIN 7; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: NSP7; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: PRODUCT RNA; COMPND 18 CHAIN: P; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 5; COMPND 21 MOLECULE: TEMPLATE RNA; COMPND 22 CHAIN: T; COMPND 23 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: SPODOPTERA AFF. FRUGIPERDA 1 BOLD-2017; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 2449148; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 11 2; SOURCE 12 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 13 ORGANISM_TAXID: 2697049; SOURCE 14 GENE: REP, 1A-1B; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 19 2; SOURCE 20 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 21 ORGANISM_TAXID: 2697049; SOURCE 22 GENE: REP, 1A-1B; SOURCE 23 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 24 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 25 MOL_ID: 4; SOURCE 26 SYNTHETIC: YES; SOURCE 27 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 28 ORGANISM_TAXID: 32630; SOURCE 29 MOL_ID: 5; SOURCE 30 SYNTHETIC: YES; SOURCE 31 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 32 ORGANISM_TAXID: 32630 KEYWDS SARS-COV-2, RNA-DEPENDENT RNA POLYMERASE, MOLNUPIRAVIR (NHC), VIRAL KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR F.KABINGER,C.STILLER,J.SCHMITZOVA,C.DIENEMANN,G.KOKIC,H.S.HILLEN, AUTHOR 2 C.HOEBARTNER,P.CRAMER REVDAT 2 29-SEP-21 7OZU 1 JRNL REVDAT 1 18-AUG-21 7OZU 0 JRNL AUTH F.KABINGER,C.STILLER,J.SCHMITZOVA,C.DIENEMANN,G.KOKIC, JRNL AUTH 2 H.S.HILLEN,C.HOBARTNER,P.CRAMER JRNL TITL MECHANISM OF MOLNUPIRAVIR-INDUCED SARS-COV-2 MUTAGENESIS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 28 740 2021 JRNL REFN ESSN 1545-9985 JRNL PMID 34381216 JRNL DOI 10.1038/S41594-021-00651-0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.KABINGER,C.STILLER,J.SCHMITZOVA,C.DIENEMANN,H.S.HILLEN, REMARK 1 AUTH 2 C.HOBARTNER,P.CRAMER REMARK 1 TITL MECHANISM OF MOLNUPIRAVIR-INDUCED SARS-COV-2 MUTAGENESIS REMARK 1 REF BIORXIV 2021 REMARK 1 REFN REMARK 1 DOI 10.1101/2021.05.11.443555 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.300 REMARK 3 NUMBER OF PARTICLES : 373938 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7OZU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1292116707. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : RDRP REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5960.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -91.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, P, T 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 SER A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 ALA A 4 REMARK 465 GLN A 5 REMARK 465 SER A 6 REMARK 465 PHE A 7 REMARK 465 LEU A 8 REMARK 465 ASN A 9 REMARK 465 ARG A 10 REMARK 465 VAL A 11 REMARK 465 CYS A 12 REMARK 465 GLY A 13 REMARK 465 VAL A 14 REMARK 465 SER A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 ARG A 18 REMARK 465 LEU A 19 REMARK 465 THR A 20 REMARK 465 PRO A 21 REMARK 465 CYS A 22 REMARK 465 GLY A 23 REMARK 465 THR A 24 REMARK 465 GLY A 25 REMARK 465 THR A 26 REMARK 465 SER A 27 REMARK 465 THR A 28 REMARK 465 ASP A 29 REMARK 465 VAL A 30 REMARK 465 THR A 51 REMARK 465 ASN A 52 REMARK 465 CYS A 53 REMARK 465 CYS A 54 REMARK 465 ARG A 55 REMARK 465 PHE A 56 REMARK 465 GLN A 57 REMARK 465 GLU A 58 REMARK 465 LYS A 59 REMARK 465 ASP A 60 REMARK 465 GLU A 61 REMARK 465 ASP A 62 REMARK 465 ASP A 63 REMARK 465 ASN A 64 REMARK 465 LEU A 65 REMARK 465 ILE A 66 REMARK 465 ASP A 67 REMARK 465 SER A 68 REMARK 465 TYR A 69 REMARK 465 PHE A 70 REMARK 465 VAL A 71 REMARK 465 VAL A 72 REMARK 465 LYS A 73 REMARK 465 ARG A 74 REMARK 465 HIS A 75 REMARK 465 THR A 76 REMARK 465 PHE A 77 REMARK 465 SER A 78 REMARK 465 ASN A 79 REMARK 465 TYR A 80 REMARK 465 GLN A 81 REMARK 465 HIS A 82 REMARK 465 GLU A 83 REMARK 465 GLU A 84 REMARK 465 THR A 85 REMARK 465 ILE A 86 REMARK 465 TYR A 87 REMARK 465 ASN A 88 REMARK 465 LEU A 89 REMARK 465 LEU A 90 REMARK 465 LYS A 91 REMARK 465 ASP A 92 REMARK 465 CYS A 93 REMARK 465 PRO A 94 REMARK 465 ALA A 95 REMARK 465 VAL A 96 REMARK 465 ALA A 97 REMARK 465 LYS A 98 REMARK 465 HIS A 99 REMARK 465 ASP A 100 REMARK 465 PHE A 101 REMARK 465 PHE A 102 REMARK 465 LYS A 103 REMARK 465 PHE A 104 REMARK 465 ARG A 105 REMARK 465 ILE A 106 REMARK 465 ASP A 107 REMARK 465 GLY A 108 REMARK 465 ASP A 109 REMARK 465 MET A 110 REMARK 465 VAL A 111 REMARK 465 PRO A 112 REMARK 465 HIS A 113 REMARK 465 ILE A 114 REMARK 465 SER A 115 REMARK 465 ARG A 116 REMARK 465 GLN A 117 REMARK 465 HIS A 362 REMARK 465 SER A 363 REMARK 465 SER A 364 REMARK 465 ARG A 365 REMARK 465 LEU A 366 REMARK 465 GLY A 897 REMARK 465 HIS A 898 REMARK 465 MET A 899 REMARK 465 LEU A 900 REMARK 465 ASP A 901 REMARK 465 MET A 902 REMARK 465 TYR A 903 REMARK 465 SER A 904 REMARK 465 VAL A 905 REMARK 465 MET A 906 REMARK 465 LEU A 907 REMARK 465 THR A 908 REMARK 465 ASN A 909 REMARK 465 VAL A 930 REMARK 465 LEU A 931 REMARK 465 GLN A 932 REMARK 465 MET B -18 REMARK 465 GLY B -17 REMARK 465 SER B -16 REMARK 465 SER B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 GLU B -8 REMARK 465 ASN B -7 REMARK 465 LEU B -6 REMARK 465 TYR B -5 REMARK 465 PHE B -4 REMARK 465 GLN B -3 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 ALA B 1 REMARK 465 ILE B 2 REMARK 465 ALA B 3 REMARK 465 SER B 4 REMARK 465 GLU B 5 REMARK 465 PHE B 6 REMARK 465 SER B 7 REMARK 465 SER B 8 REMARK 465 LEU B 9 REMARK 465 PRO B 10 REMARK 465 SER B 11 REMARK 465 TYR B 12 REMARK 465 ALA B 13 REMARK 465 ALA B 14 REMARK 465 PHE B 15 REMARK 465 ALA B 16 REMARK 465 THR B 17 REMARK 465 ALA B 18 REMARK 465 GLN B 19 REMARK 465 GLU B 20 REMARK 465 ALA B 21 REMARK 465 TYR B 22 REMARK 465 GLU B 23 REMARK 465 GLN B 24 REMARK 465 ALA B 25 REMARK 465 VAL B 26 REMARK 465 ALA B 27 REMARK 465 ASN B 28 REMARK 465 GLY B 29 REMARK 465 ASP B 30 REMARK 465 SER B 31 REMARK 465 GLU B 32 REMARK 465 VAL B 33 REMARK 465 VAL B 34 REMARK 465 LEU B 35 REMARK 465 LYS B 36 REMARK 465 LYS B 37 REMARK 465 LEU B 38 REMARK 465 LYS B 39 REMARK 465 LYS B 40 REMARK 465 SER B 41 REMARK 465 LEU B 42 REMARK 465 ASN B 43 REMARK 465 VAL B 44 REMARK 465 ALA B 45 REMARK 465 LYS B 46 REMARK 465 SER B 47 REMARK 465 GLU B 48 REMARK 465 PHE B 49 REMARK 465 ASP B 50 REMARK 465 ARG B 51 REMARK 465 ASP B 52 REMARK 465 ALA B 53 REMARK 465 ALA B 54 REMARK 465 MET B 55 REMARK 465 GLN B 56 REMARK 465 ARG B 57 REMARK 465 LYS B 58 REMARK 465 LEU B 59 REMARK 465 GLU B 60 REMARK 465 LYS B 61 REMARK 465 MET B 62 REMARK 465 ALA B 63 REMARK 465 ASP B 64 REMARK 465 GLN B 65 REMARK 465 ALA B 66 REMARK 465 MET B 67 REMARK 465 THR B 68 REMARK 465 GLN B 69 REMARK 465 MET B 70 REMARK 465 TYR B 71 REMARK 465 LYS B 72 REMARK 465 GLN B 73 REMARK 465 ALA B 74 REMARK 465 ARG B 75 REMARK 465 SER B 76 REMARK 465 ASN B 192 REMARK 465 SER B 193 REMARK 465 ALA B 194 REMARK 465 VAL B 195 REMARK 465 LYS B 196 REMARK 465 LEU B 197 REMARK 465 GLN B 198 REMARK 465 SER C -2 REMARK 465 ASN C -1 REMARK 465 ALA C 0 REMARK 465 GLN C 63 REMARK 465 GLY C 64 REMARK 465 ALA C 65 REMARK 465 VAL C 66 REMARK 465 ASP C 67 REMARK 465 ILE C 68 REMARK 465 ASN C 69 REMARK 465 LYS C 70 REMARK 465 LEU C 71 REMARK 465 CYS C 72 REMARK 465 GLU C 73 REMARK 465 GLU C 74 REMARK 465 MET C 75 REMARK 465 LEU C 76 REMARK 465 ASP C 77 REMARK 465 ASN C 78 REMARK 465 ARG C 79 REMARK 465 ALA C 80 REMARK 465 THR C 81 REMARK 465 U P -16 REMARK 465 U P -15 REMARK 465 G P -14 REMARK 465 G P -13 REMARK 465 U P -12 REMARK 465 C P -11 REMARK 465 U P -10 REMARK 465 C P -9 REMARK 465 A P -8 REMARK 465 A P -7 REMARK 465 U P -6 REMARK 465 A P -5 REMARK 465 C P -4 REMARK 465 G P -3 REMARK 465 G P -2 REMARK 465 U P -1 REMARK 465 A P 0 REMARK 465 U P 1 REMARK 465 G P 2 REMARK 465 A P 3 REMARK 465 G P 4 REMARK 465 C P 5 REMARK 465 C T 19 REMARK 465 U T 20 REMARK 465 C T 21 REMARK 465 A T 22 REMARK 465 U T 23 REMARK 465 A T 24 REMARK 465 C T 25 REMARK 465 C T 26 REMARK 465 G T 27 REMARK 465 U T 28 REMARK 465 A T 29 REMARK 465 U T 30 REMARK 465 U T 31 REMARK 465 G T 32 REMARK 465 A T 33 REMARK 465 G T 34 REMARK 465 A T 35 REMARK 465 C T 36 REMARK 465 C T 37 REMARK 465 U T 38 REMARK 465 U T 39 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 A T 10 O3' - P - O5' ANGL. DEV. = -11.9 DEGREES REMARK 500 A T 10 O3' - P - OP2 ANGL. DEV. = 9.1 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 CYS A 152 -169.77 -161.63 REMARK 500 PRO A 264 -180.00 -69.09 REMARK 500 TYR A 286 -60.97 -94.45 REMARK 500 CYS A 298 1.96 -68.02 REMARK 500 ASN A 300 35.37 -99.56 REMARK 500 ASP A 303 -168.17 -161.18 REMARK 500 ASP A 499 33.81 -99.01 REMARK 500 VAL A 662 -55.50 -128.71 REMARK 500 SER A 759 -26.05 63.31 REMARK 500 ASP A 760 -24.47 -145.29 REMARK 500 LYS A 849 38.42 -98.57 REMARK 500 THR B 141 -60.19 -94.95 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 A2000 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 295 ND1 REMARK 620 2 CYS A 301 SG 113.3 REMARK 620 3 CYS A 306 SG 106.9 112.0 REMARK 620 4 CYS A 310 SG 113.5 95.4 115.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 487 SG REMARK 620 2 HIS A 642 ND1 98.1 REMARK 620 3 CYS A 645 SG 109.7 87.3 REMARK 620 4 CYS A 646 SG 100.0 145.5 113.5 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13135 RELATED DB: EMDB REMARK 900 SARS-COV-2 RDRP WITH MOLNUPIRAVIR/ NHC IN THE TEMPLATE STRAND BASE- REMARK 900 PAIRED WITH A DBREF 7OZU A 1 932 UNP P0DTD1 R1AB_SARS2 4393 5324 DBREF 7OZU B 1 198 UNP P0DTD1 R1AB_SARS2 3943 4140 DBREF 7OZU C 1 81 UNP P0DTD1 R1AB_SARS2 3860 3940 DBREF 7OZU P -16 15 PDB 7OZU 7OZU -16 15 DBREF 7OZU T 7 39 PDB 7OZU 7OZU 7 39 SEQADV 7OZU MET B -18 UNP P0DTD1 INITIATING METHIONINE SEQADV 7OZU GLY B -17 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU SER B -16 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU SER B -15 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU HIS B -14 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU HIS B -13 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU HIS B -12 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU HIS B -11 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU HIS B -10 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU HIS B -9 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU GLU B -8 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU ASN B -7 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU LEU B -6 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU TYR B -5 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU PHE B -4 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU GLN B -3 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU SER B -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU ASN B -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU ALA B 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU SER C -2 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU ASN C -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7OZU ALA C 0 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 932 SER ALA ASP ALA GLN SER PHE LEU ASN ARG VAL CYS GLY SEQRES 2 A 932 VAL SER ALA ALA ARG LEU THR PRO CYS GLY THR GLY THR SEQRES 3 A 932 SER THR ASP VAL VAL TYR ARG ALA PHE ASP ILE TYR ASN SEQRES 4 A 932 ASP LYS VAL ALA GLY PHE ALA LYS PHE LEU LYS THR ASN SEQRES 5 A 932 CYS CYS ARG PHE GLN GLU LYS ASP GLU ASP ASP ASN LEU SEQRES 6 A 932 ILE ASP SER TYR PHE VAL VAL LYS ARG HIS THR PHE SER SEQRES 7 A 932 ASN TYR GLN HIS GLU GLU THR ILE TYR ASN LEU LEU LYS SEQRES 8 A 932 ASP CYS PRO ALA VAL ALA LYS HIS ASP PHE PHE LYS PHE SEQRES 9 A 932 ARG ILE ASP GLY ASP MET VAL PRO HIS ILE SER ARG GLN SEQRES 10 A 932 ARG LEU THR LYS TYR THR MET ALA ASP LEU VAL TYR ALA SEQRES 11 A 932 LEU ARG HIS PHE ASP GLU GLY ASN CYS ASP THR LEU LYS SEQRES 12 A 932 GLU ILE LEU VAL THR TYR ASN CYS CYS ASP ASP ASP TYR SEQRES 13 A 932 PHE ASN LYS LYS ASP TRP TYR ASP PHE VAL GLU ASN PRO SEQRES 14 A 932 ASP ILE LEU ARG VAL TYR ALA ASN LEU GLY GLU ARG VAL SEQRES 15 A 932 ARG GLN ALA LEU LEU LYS THR VAL GLN PHE CYS ASP ALA SEQRES 16 A 932 MET ARG ASN ALA GLY ILE VAL GLY VAL LEU THR LEU ASP SEQRES 17 A 932 ASN GLN ASP LEU ASN GLY ASN TRP TYR ASP PHE GLY ASP SEQRES 18 A 932 PHE ILE GLN THR THR PRO GLY SER GLY VAL PRO VAL VAL SEQRES 19 A 932 ASP SER TYR TYR SER LEU LEU MET PRO ILE LEU THR LEU SEQRES 20 A 932 THR ARG ALA LEU THR ALA GLU SER HIS VAL ASP THR ASP SEQRES 21 A 932 LEU THR LYS PRO TYR ILE LYS TRP ASP LEU LEU LYS TYR SEQRES 22 A 932 ASP PHE THR GLU GLU ARG LEU LYS LEU PHE ASP ARG TYR SEQRES 23 A 932 PHE LYS TYR TRP ASP GLN THR TYR HIS PRO ASN CYS VAL SEQRES 24 A 932 ASN CYS LEU ASP ASP ARG CYS ILE LEU HIS CYS ALA ASN SEQRES 25 A 932 PHE ASN VAL LEU PHE SER THR VAL PHE PRO PRO THR SER SEQRES 26 A 932 PHE GLY PRO LEU VAL ARG LYS ILE PHE VAL ASP GLY VAL SEQRES 27 A 932 PRO PHE VAL VAL SER THR GLY TYR HIS PHE ARG GLU LEU SEQRES 28 A 932 GLY VAL VAL HIS ASN GLN ASP VAL ASN LEU HIS SER SER SEQRES 29 A 932 ARG LEU SER PHE LYS GLU LEU LEU VAL TYR ALA ALA ASP SEQRES 30 A 932 PRO ALA MET HIS ALA ALA SER GLY ASN LEU LEU LEU ASP SEQRES 31 A 932 LYS ARG THR THR CYS PHE SER VAL ALA ALA LEU THR ASN SEQRES 32 A 932 ASN VAL ALA PHE GLN THR VAL LYS PRO GLY ASN PHE ASN SEQRES 33 A 932 LYS ASP PHE TYR ASP PHE ALA VAL SER LYS GLY PHE PHE SEQRES 34 A 932 LYS GLU GLY SER SER VAL GLU LEU LYS HIS PHE PHE PHE SEQRES 35 A 932 ALA GLN ASP GLY ASN ALA ALA ILE SER ASP TYR ASP TYR SEQRES 36 A 932 TYR ARG TYR ASN LEU PRO THR MET CYS ASP ILE ARG GLN SEQRES 37 A 932 LEU LEU PHE VAL VAL GLU VAL VAL ASP LYS TYR PHE ASP SEQRES 38 A 932 CYS TYR ASP GLY GLY CYS ILE ASN ALA ASN GLN VAL ILE SEQRES 39 A 932 VAL ASN ASN LEU ASP LYS SER ALA GLY PHE PRO PHE ASN SEQRES 40 A 932 LYS TRP GLY LYS ALA ARG LEU TYR TYR ASP SER MET SER SEQRES 41 A 932 TYR GLU ASP GLN ASP ALA LEU PHE ALA TYR THR LYS ARG SEQRES 42 A 932 ASN VAL ILE PRO THR ILE THR GLN MET ASN LEU LYS TYR SEQRES 43 A 932 ALA ILE SER ALA LYS ASN ARG ALA ARG THR VAL ALA GLY SEQRES 44 A 932 VAL SER ILE CYS SER THR MET THR ASN ARG GLN PHE HIS SEQRES 45 A 932 GLN LYS LEU LEU LYS SER ILE ALA ALA THR ARG GLY ALA SEQRES 46 A 932 THR VAL VAL ILE GLY THR SER LYS PHE TYR GLY GLY TRP SEQRES 47 A 932 HIS ASN MET LEU LYS THR VAL TYR SER ASP VAL GLU ASN SEQRES 48 A 932 PRO HIS LEU MET GLY TRP ASP TYR PRO LYS CYS ASP ARG SEQRES 49 A 932 ALA MET PRO ASN MET LEU ARG ILE MET ALA SER LEU VAL SEQRES 50 A 932 LEU ALA ARG LYS HIS THR THR CYS CYS SER LEU SER HIS SEQRES 51 A 932 ARG PHE TYR ARG LEU ALA ASN GLU CYS ALA GLN VAL LEU SEQRES 52 A 932 SER GLU MET VAL MET CYS GLY GLY SER LEU TYR VAL LYS SEQRES 53 A 932 PRO GLY GLY THR SER SER GLY ASP ALA THR THR ALA TYR SEQRES 54 A 932 ALA ASN SER VAL PHE ASN ILE CYS GLN ALA VAL THR ALA SEQRES 55 A 932 ASN VAL ASN ALA LEU LEU SER THR ASP GLY ASN LYS ILE SEQRES 56 A 932 ALA ASP LYS TYR VAL ARG ASN LEU GLN HIS ARG LEU TYR SEQRES 57 A 932 GLU CYS LEU TYR ARG ASN ARG ASP VAL ASP THR ASP PHE SEQRES 58 A 932 VAL ASN GLU PHE TYR ALA TYR LEU ARG LYS HIS PHE SER SEQRES 59 A 932 MET MET ILE LEU SER ASP ASP ALA VAL VAL CYS PHE ASN SEQRES 60 A 932 SER THR TYR ALA SER GLN GLY LEU VAL ALA SER ILE LYS SEQRES 61 A 932 ASN PHE LYS SER VAL LEU TYR TYR GLN ASN ASN VAL PHE SEQRES 62 A 932 MET SER GLU ALA LYS CYS TRP THR GLU THR ASP LEU THR SEQRES 63 A 932 LYS GLY PRO HIS GLU PHE CYS SER GLN HIS THR MET LEU SEQRES 64 A 932 VAL LYS GLN GLY ASP ASP TYR VAL TYR LEU PRO TYR PRO SEQRES 65 A 932 ASP PRO SER ARG ILE LEU GLY ALA GLY CYS PHE VAL ASP SEQRES 66 A 932 ASP ILE VAL LYS THR ASP GLY THR LEU MET ILE GLU ARG SEQRES 67 A 932 PHE VAL SER LEU ALA ILE ASP ALA TYR PRO LEU THR LYS SEQRES 68 A 932 HIS PRO ASN GLN GLU TYR ALA ASP VAL PHE HIS LEU TYR SEQRES 69 A 932 LEU GLN TYR ILE ARG LYS LEU HIS ASP GLU LEU THR GLY SEQRES 70 A 932 HIS MET LEU ASP MET TYR SER VAL MET LEU THR ASN ASP SEQRES 71 A 932 ASN THR SER ARG TYR TRP GLU PRO GLU PHE TYR GLU ALA SEQRES 72 A 932 MET TYR THR PRO HIS THR VAL LEU GLN SEQRES 1 B 217 MET GLY SER SER HIS HIS HIS HIS HIS HIS GLU ASN LEU SEQRES 2 B 217 TYR PHE GLN SER ASN ALA ALA ILE ALA SER GLU PHE SER SEQRES 3 B 217 SER LEU PRO SER TYR ALA ALA PHE ALA THR ALA GLN GLU SEQRES 4 B 217 ALA TYR GLU GLN ALA VAL ALA ASN GLY ASP SER GLU VAL SEQRES 5 B 217 VAL LEU LYS LYS LEU LYS LYS SER LEU ASN VAL ALA LYS SEQRES 6 B 217 SER GLU PHE ASP ARG ASP ALA ALA MET GLN ARG LYS LEU SEQRES 7 B 217 GLU LYS MET ALA ASP GLN ALA MET THR GLN MET TYR LYS SEQRES 8 B 217 GLN ALA ARG SER GLU ASP LYS ARG ALA LYS VAL THR SER SEQRES 9 B 217 ALA MET GLN THR MET LEU PHE THR MET LEU ARG LYS LEU SEQRES 10 B 217 ASP ASN ASP ALA LEU ASN ASN ILE ILE ASN ASN ALA ARG SEQRES 11 B 217 ASP GLY CYS VAL PRO LEU ASN ILE ILE PRO LEU THR THR SEQRES 12 B 217 ALA ALA LYS LEU MET VAL VAL ILE PRO ASP TYR ASN THR SEQRES 13 B 217 TYR LYS ASN THR CYS ASP GLY THR THR PHE THR TYR ALA SEQRES 14 B 217 SER ALA LEU TRP GLU ILE GLN GLN VAL VAL ASP ALA ASP SEQRES 15 B 217 SER LYS ILE VAL GLN LEU SER GLU ILE SER MET ASP ASN SEQRES 16 B 217 SER PRO ASN LEU ALA TRP PRO LEU ILE VAL THR ALA LEU SEQRES 17 B 217 ARG ALA ASN SER ALA VAL LYS LEU GLN SEQRES 1 C 84 SER ASN ALA SER LYS MET SER ASP VAL LYS CYS THR SER SEQRES 2 C 84 VAL VAL LEU LEU SER VAL LEU GLN GLN LEU ARG VAL GLU SEQRES 3 C 84 SER SER SER LYS LEU TRP ALA GLN CYS VAL GLN LEU HIS SEQRES 4 C 84 ASN ASP ILE LEU LEU ALA LYS ASP THR THR GLU ALA PHE SEQRES 5 C 84 GLU LYS MET VAL SER LEU LEU SER VAL LEU LEU SER MET SEQRES 6 C 84 GLN GLY ALA VAL ASP ILE ASN LYS LEU CYS GLU GLU MET SEQRES 7 C 84 LEU ASP ASN ARG ALA THR SEQRES 1 P 32 U U G G U C U C A A U A C SEQRES 2 P 32 G G U A U G A G C C U A C SEQRES 3 P 32 G C A G U A SEQRES 1 T 33 G G 7OK A C U G C G U A G C SEQRES 2 T 33 U C A U A C C G U A U U G SEQRES 3 T 33 A G A C C U U HET 7OK T 9 21 HET ZN A2000 1 HET ZN A2001 1 HETNAM 7OK N-HYDROXYCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) TAUTOMER HETNAM ZN ZINC ION HETSYN 7OK [(2R,3S,4R,5R)-5-[(4E)-4-HYDROXYIMINO-2-OXIDANYLIDENE- HETSYN 2 7OK PYRIMIDIN-1-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL HETSYN 3 7OK DIHYDROGEN PHOSPHATE FORMUL 5 7OK C9 H14 N3 O9 P FORMUL 6 ZN 2(ZN 2+) HELIX 1 AA1 THR A 123 HIS A 133 1 11 HELIX 2 AA2 CYS A 139 TYR A 149 1 11 HELIX 3 AA3 ASP A 153 LYS A 159 1 7 HELIX 4 AA4 ASP A 170 ALA A 199 1 30 HELIX 5 AA5 THR A 206 GLN A 210 5 5 HELIX 6 AA6 VAL A 234 THR A 248 1 15 HELIX 7 AA7 ARG A 249 ASP A 260 5 12 HELIX 8 AA8 PHE A 275 TYR A 286 1 12 HELIX 9 AA9 ASN A 297 CYS A 301 5 5 HELIX 10 AB1 ASP A 303 SER A 318 1 16 HELIX 11 AB2 PHE A 368 ASP A 377 1 10 HELIX 12 AB3 ASP A 377 GLY A 385 1 9 HELIX 13 AB4 ASN A 416 LYS A 426 1 11 HELIX 14 AB5 ASN A 447 ASP A 454 1 8 HELIX 15 AB6 TYR A 455 ASN A 459 5 5 HELIX 16 AB7 ASP A 465 TYR A 479 1 15 HELIX 17 AB8 ASN A 489 VAL A 493 5 5 HELIX 18 AB9 PRO A 505 TRP A 509 5 5 HELIX 19 AC1 LYS A 511 MET A 519 1 9 HELIX 20 AC2 SER A 520 LYS A 532 1 13 HELIX 21 AC3 SER A 561 ALA A 581 1 21 HELIX 22 AC4 GLY A 596 TYR A 606 1 11 HELIX 23 AC5 LYS A 621 MET A 626 1 6 HELIX 24 AC6 PRO A 627 ALA A 639 1 13 HELIX 25 AC7 SER A 647 VAL A 662 1 16 HELIX 26 AC8 THR A 686 THR A 710 1 25 HELIX 27 AC9 ASP A 717 TYR A 732 1 16 HELIX 28 AD1 ASP A 738 HIS A 752 1 15 HELIX 29 AD2 SER A 768 GLY A 774 1 7 HELIX 30 AD3 SER A 778 GLN A 789 1 12 HELIX 31 AD4 SER A 795 CYS A 799 5 5 HELIX 32 AD5 ASP A 833 PHE A 843 1 11 HELIX 33 AD6 ASP A 846 ASP A 851 5 6 HELIX 34 AD7 GLY A 852 ALA A 866 1 15 HELIX 35 AD8 TYR A 867 HIS A 872 5 6 HELIX 36 AD9 ASN A 874 THR A 896 1 23 HELIX 37 AE1 ASN A 911 TRP A 916 5 6 HELIX 38 AE2 PRO A 918 ALA A 923 1 6 HELIX 39 AE3 MET A 924 THR A 926 5 3 HELIX 40 AE4 ASP B 78 LEU B 98 1 21 HELIX 41 AE5 ASP B 99 ALA B 110 1 12 HELIX 42 AE6 ILE B 119 ALA B 125 1 7 HELIX 43 AE7 ASP B 134 ASP B 143 1 10 HELIX 44 AE8 ASN B 176 LEU B 180 5 5 HELIX 45 AE9 LYS C 2 LEU C 20 1 19 HELIX 46 AF1 ARG C 21 SER C 24 5 4 HELIX 47 AF2 SER C 25 ALA C 42 1 18 HELIX 48 AF3 ASP C 44 MET C 62 1 19 SHEET 1 AA1 2 TYR A 32 TYR A 38 0 SHEET 2 AA1 2 ALA A 43 LEU A 49 -1 O ALA A 46 N PHE A 35 SHEET 1 AA2 2 ILE A 201 VAL A 202 0 SHEET 2 AA2 2 ILE A 223 GLN A 224 -1 O ILE A 223 N VAL A 202 SHEET 1 AA3 4 GLY A 352 HIS A 355 0 SHEET 2 AA3 4 VAL A 338 PHE A 348 -1 N TYR A 346 O VAL A 354 SHEET 3 AA3 4 GLY A 327 VAL A 335 -1 N LEU A 329 O THR A 344 SHEET 4 AA3 4 VAL B 115 PRO B 116 -1 O VAL B 115 N VAL A 330 SHEET 1 AA4 5 LEU A 387 ASP A 390 0 SHEET 2 AA4 5 LYS B 127 ILE B 132 1 O MET B 129 N LEU A 389 SHEET 3 AA4 5 LEU B 184 ARG B 190 -1 O ALA B 188 N LEU B 128 SHEET 4 AA4 5 ALA B 152 VAL B 160 -1 N VAL B 160 O ILE B 185 SHEET 5 AA4 5 THR B 146 TYR B 149 -1 N TYR B 149 O ALA B 152 SHEET 1 AA5 5 SER A 397 ALA A 400 0 SHEET 2 AA5 5 SER A 672 VAL A 675 -1 O LEU A 673 N VAL A 398 SHEET 3 AA5 5 MET A 666 CYS A 669 -1 N VAL A 667 O TYR A 674 SHEET 4 AA5 5 ILE A 539 LEU A 544 1 N THR A 540 O MET A 666 SHEET 5 AA5 5 THR A 556 GLY A 559 -1 O VAL A 557 N ASN A 543 SHEET 1 AA6 4 PHE A 753 LEU A 758 0 SHEET 2 AA6 4 ASP A 761 ASN A 767 -1 O CYS A 765 N SER A 754 SHEET 3 AA6 4 PRO A 612 TRP A 617 -1 N MET A 615 O VAL A 764 SHEET 4 AA6 4 TRP A 800 GLU A 802 -1 O GLU A 802 N LEU A 614 SHEET 1 AA7 2 HIS A 816 GLN A 822 0 SHEET 2 AA7 2 ASP A 825 TYR A 831 -1 O TYR A 831 N HIS A 816 LINK O3' G T 8 P 7OK T 9 1555 1555 1.59 LINK O3' 7OK T 9 P A T 10 1555 1555 1.59 LINK ND1 HIS A 295 ZN ZN A2000 1555 1555 2.08 LINK SG CYS A 301 ZN ZN A2000 1555 1555 2.31 LINK SG CYS A 306 ZN ZN A2000 1555 1555 2.30 LINK SG CYS A 310 ZN ZN A2000 1555 1555 2.30 LINK SG CYS A 487 ZN ZN A2001 1555 1555 2.28 LINK ND1 HIS A 642 ZN ZN A2001 1555 1555 2.31 LINK SG CYS A 645 ZN ZN A2001 1555 1555 2.30 LINK SG CYS A 646 ZN ZN A2001 1555 1555 2.29 CISPEP 1 PHE A 504 PRO A 505 0 -1.12 CISPEP 2 TRP B 182 PRO B 183 0 0.80 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000