7CTT

Cryo-EM structure of Favipiravir bound to replicating polymerase complex of SARS-CoV-2 in the pre-catalytic state.


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8092559 3001272 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8092559 3001272 SCOP2B (2022-06-29)
BSCOP2B SuperfamilySARS coronavirus NSP8-like 8092561 3000855 SCOP2B (2022-06-29)
CSCOP2B SuperfamilySARS coronavirus NSP7-like 8092555 3001013 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Bnsp8e7cttB1 A: beta barrelsX: Coronavirus NSP8-like (From Topology)H: Coronavirus NSP8-like (From Topology)T: Coronavirus NSP8-likeF: nsp8ECOD (1.6)
Cnsp7e7cttC1 A: alpha bundlesX: immunoglobulin/albumin-binding domain-likeH: Coronavirus NSP7-like (From Topology)T: Coronavirus NSP7-likeF: nsp7ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF00680Viral RNA-dependent RNA polymerase (RdRP_1)Viral RNA-dependent RNA polymerase- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
RNA-directed RNA polymerase
B, D
Non-structural protein 8
Non-structural protein 7
E [auth Q]Primer-RNA (5'-R(P*UP*UP*CP*UP*CP*CP*UP*AP*AP*GP*AP*AP*GP*CP*UP*A)-3')---
F [auth T]Template-RNA (5'-R(P*AP*CP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*GP*GP*AP*GP*AP*A)-3')---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR022733DPUP/SUD, C-terminal, betacoronavirusDomain
IPR042515Non-structural protein NSP15, N-terminal domain superfamily, coronavirusHomologous Superfamily
IPR043174Non-structural protein NSP15, middle domain superfamilyHomologous Superfamily
IPR044315Nonstructural protein 14, betacoronavirusDomain
IPR038123Non-structural protein NSP4, C-terminal superfamily, coronavirusHomologous Superfamily
IPR042570Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirusHomologous Superfamily
IPR043178Papain-like protease, thumb domain superfamily, coronavirusHomologous Superfamily
IPR046441RNA-dependent RNA polymerase, coronavirusDomain
IPR044863Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domainDomain
IPR044343Nonstructural protein 13, 1B domain, coronavirusDomain
IPR038166Polyprotein cleavage domain PL2pro superfamily, betacoronavirusHomologous Superfamily
IPR037227Endoribonuclease EndoU-likeHomologous Superfamily
IPR027352Nonstructural protein 13, zinc-binding domain, coronavirus-likeDomain
IPR009003Peptidase S1, PA clanHomologous Superfamily
IPR013016Peptidase C16, coronavirusDomain
IPR009466Non-structural protein 14, coronavirusDomain
IPR044357NSP3, first ubiquitin-like (Ubl) domain, coronavirusDomain
IPR046436Nidovirus 3'-5' exoribonuclease domainDomain
IPR047570NSP12, interface domain, coronavirusDomain
IPR018995RNA synthesis protein NSP10, coronavirusDomain
IPR043615Nonstructural protein 2, N-terminal domain, coronavirusDomain
IPR050534Coronaviruses polyprotein 1abFamily
IPR043177Papain-like protease, N-terminal domain superfamily, coronavirusHomologous Superfamily
IPR043606Coronavirus replicase NSP15, N-terminal oligomerizationDomain
IPR044330Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirusDomain
IPR041679DNA2/NAM7 helicase-like, C-terminalDomain
IPR024375Non-structural protein NSP3, SUD-M domain, betacoronavirusDomain
IPR014828Non-structural protein NSP7, coronavirusDomain
IPR043503Papain-like viral protease, palm and finger domains, coronavirusHomologous Superfamily
IPR014829Non-structural protein NSP8, coronavirusDomain
IPR036499Non-structural protein NSP9 superfamily, coronavirusHomologous Superfamily
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
IPR044389Non-structural protein 2, SARS-CoV-likeDomain
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
IPR008740Peptidase C30, coronavirusDomain
IPR036333RNA synthesis protein NSP10 superfamily, coronavirusHomologous Superfamily
IPR047573Non-structural protein 2, middle domain, coronavirusDomain
IPR049894Coronavirus NSP3, 3Ecto domainDomain
IPR043472Macro domain-likeHomologous Superfamily
IPR043609NendoU domain, nidovirusDomain
IPR032592Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirusDomain
IPR043613Non-structural protein 2, C-terminal domain, coronavirusDomain
IPR038083Non-structural protein NSP3A domain-like superfamilyHomologous Superfamily
IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
IPR044351RNA-dependent RNA polymerase, SARS-CoV-likeDomain
IPR024358Non-structural protein NSP3, N-terminal, betacoronavirusDomain
IPR048673Nonstructural protein 13, stalk domain, coronavirusDomain
IPR046435NSP14, guanine-N7-methyltransferase domain, coronavirusDomain
IPR009469RNA-dependent RNA polymerase, N-terminal, coronavirusDomain
IPR043611Coronavirus replicase NSP3, C-terminalDomain
IPR044864Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirusDomain
IPR047566Coronavirus replicase NSP3, Y domainDomain
IPR048672Nonstructural protein 13, zinc-binding domain, coronavirusDomain
IPR043612Non-structural protein NSP4, N-terminal, coronavirusDomain
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
IPR043608Nonstructural protein 15, middle domain, coronavirusDomain
IPR044353NSP3, second ubiquitin-like (Ubl) domain, coronavirusDomain
IPR037204Non-structural protein NSP7 superfamily, coronavirusHomologous Superfamily
IPR046443NSP1, globular domain, alpha/betacoronavirusDomain
IPR043610Non-structural protein 6, coronavirusDomain
IPR027351(+) RNA virus helicase core domainDomain
IPR044322Nonstructural protein 15, middle domain, alpha/betacoronavirusDomain
IPR009461Non-structural protein NSP16, coronavirus-likeDomain
IPR043477Peptidase C30, domain 3, coronavirusHomologous Superfamily
IPR043478Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirusHomologous Superfamily
IPR038400Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirusHomologous Superfamily
IPR046442NSP1, C-terminal domain, betacoronavirusDomain
IPR001205RNA-directed RNA polymerase, C-terminal domainDomain
IPR044401NSP15, NendoU domain, coronavirusDomain
IPR014822Non-structural protein NSP9, coronavirusDomain
IPR038030NSP1 globular domain superfamily, betacoronavirusHomologous Superfamily
IPR021590NSP1, globular domain, betacoronavirusDomain
IPR044367Non-structural protein 6, betacoronavirusDomain
IPR037230Non-structural protein NSP8 superfamily, coronavirusHomologous Superfamily
IPR046440Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domainDomain
IPR032505Non-structural protein NSP4, C-terminal, coronavirusDomain
IPR046438Nidovirus 2-O-methyltransferaseDomain
IPR002589Macro domainDomain
IPR047567Non-structural protein NSP3, group 2-specific marker domain, betacoronavirusDomain
IPR044371Non-structural protein 3, X-domain-likeDomain
IPR007094RNA-directed RNA polymerase, catalytic domainDomain
B, D
IPR022733DPUP/SUD, C-terminal, betacoronavirusDomain
B, D
IPR042515Non-structural protein NSP15, N-terminal domain superfamily, coronavirusHomologous Superfamily
B, D
IPR043174Non-structural protein NSP15, middle domain superfamilyHomologous Superfamily
B, D
IPR044315Nonstructural protein 14, betacoronavirusDomain
B, D
IPR038123Non-structural protein NSP4, C-terminal superfamily, coronavirusHomologous Superfamily
B, D
IPR042570Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirusHomologous Superfamily
B, D
IPR043178Papain-like protease, thumb domain superfamily, coronavirusHomologous Superfamily
B, D
IPR046441RNA-dependent RNA polymerase, coronavirusDomain
B, D
IPR044863Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domainDomain
B, D
IPR044343Nonstructural protein 13, 1B domain, coronavirusDomain
B, D
IPR038166Polyprotein cleavage domain PL2pro superfamily, betacoronavirusHomologous Superfamily
B, D
IPR037227Endoribonuclease EndoU-likeHomologous Superfamily
B, D
IPR027352Nonstructural protein 13, zinc-binding domain, coronavirus-likeDomain
B, D
IPR009003Peptidase S1, PA clanHomologous Superfamily
B, D
IPR013016Peptidase C16, coronavirusDomain
B, D
IPR009466Non-structural protein 14, coronavirusDomain
B, D
IPR044357NSP3, first ubiquitin-like (Ubl) domain, coronavirusDomain
B, D
IPR046436Nidovirus 3'-5' exoribonuclease domainDomain
B, D
IPR047570NSP12, interface domain, coronavirusDomain
B, D
IPR018995RNA synthesis protein NSP10, coronavirusDomain
B, D
IPR043615Nonstructural protein 2, N-terminal domain, coronavirusDomain
B, D
IPR050534Coronaviruses polyprotein 1abFamily
B, D
IPR043177Papain-like protease, N-terminal domain superfamily, coronavirusHomologous Superfamily
B, D
IPR043606Coronavirus replicase NSP15, N-terminal oligomerizationDomain
B, D
IPR044330Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirusDomain
B, D
IPR041679DNA2/NAM7 helicase-like, C-terminalDomain
B, D
IPR024375Non-structural protein NSP3, SUD-M domain, betacoronavirusDomain
B, D
IPR014828Non-structural protein NSP7, coronavirusDomain
B, D
IPR043503Papain-like viral protease, palm and finger domains, coronavirusHomologous Superfamily
B, D
IPR014829Non-structural protein NSP8, coronavirusDomain
B, D
IPR036499Non-structural protein NSP9 superfamily, coronavirusHomologous Superfamily
B, D
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
B, D
IPR044389Non-structural protein 2, SARS-CoV-likeDomain
B, D
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
B, D
IPR008740Peptidase C30, coronavirusDomain
B, D
IPR036333RNA synthesis protein NSP10 superfamily, coronavirusHomologous Superfamily
B, D
IPR047573Non-structural protein 2, middle domain, coronavirusDomain
B, D
IPR049894Coronavirus NSP3, 3Ecto domainDomain
B, D
IPR043472Macro domain-likeHomologous Superfamily
B, D
IPR043609NendoU domain, nidovirusDomain
B, D
IPR032592Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirusDomain
B, D
IPR043613Non-structural protein 2, C-terminal domain, coronavirusDomain
B, D
IPR038083Non-structural protein NSP3A domain-like superfamilyHomologous Superfamily
B, D
IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
B, D
IPR044351RNA-dependent RNA polymerase, SARS-CoV-likeDomain
B, D
IPR024358Non-structural protein NSP3, N-terminal, betacoronavirusDomain
B, D
IPR048673Nonstructural protein 13, stalk domain, coronavirusDomain
B, D
IPR046435NSP14, guanine-N7-methyltransferase domain, coronavirusDomain
B, D
IPR009469RNA-dependent RNA polymerase, N-terminal, coronavirusDomain
B, D
IPR043611Coronavirus replicase NSP3, C-terminalDomain
B, D
IPR044864Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirusDomain
B, D
IPR047566Coronavirus replicase NSP3, Y domainDomain
B, D
IPR048672Nonstructural protein 13, zinc-binding domain, coronavirusDomain
B, D
IPR043612Non-structural protein NSP4, N-terminal, coronavirusDomain
B, D
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
B, D
IPR043608Nonstructural protein 15, middle domain, coronavirusDomain
B, D
IPR044353NSP3, second ubiquitin-like (Ubl) domain, coronavirusDomain
B, D
IPR037204Non-structural protein NSP7 superfamily, coronavirusHomologous Superfamily
B, D
IPR046443NSP1, globular domain, alpha/betacoronavirusDomain
B, D
IPR043610Non-structural protein 6, coronavirusDomain
B, D
IPR027351(+) RNA virus helicase core domainDomain
B, D
IPR044322Nonstructural protein 15, middle domain, alpha/betacoronavirusDomain
B, D
IPR009461Non-structural protein NSP16, coronavirus-likeDomain
B, D
IPR043477Peptidase C30, domain 3, coronavirusHomologous Superfamily
B, D
IPR043478Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirusHomologous Superfamily
B, D
IPR038400Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirusHomologous Superfamily
B, D
IPR046442NSP1, C-terminal domain, betacoronavirusDomain
B, D
IPR001205RNA-directed RNA polymerase, C-terminal domainDomain
B, D
IPR044401NSP15, NendoU domain, coronavirusDomain
B, D
IPR014822Non-structural protein NSP9, coronavirusDomain
B, D
IPR038030NSP1 globular domain superfamily, betacoronavirusHomologous Superfamily
B, D
IPR021590NSP1, globular domain, betacoronavirusDomain
B, D
IPR044367Non-structural protein 6, betacoronavirusDomain
B, D
IPR037230Non-structural protein NSP8 superfamily, coronavirusHomologous Superfamily
B, D
IPR046440Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domainDomain
B, D
IPR032505Non-structural protein NSP4, C-terminal, coronavirusDomain
B, D
IPR046438Nidovirus 2-O-methyltransferaseDomain
B, D
IPR002589Macro domainDomain
B, D
IPR047567Non-structural protein NSP3, group 2-specific marker domain, betacoronavirusDomain
B, D
IPR044371Non-structural protein 3, X-domain-likeDomain
B, D
IPR007094RNA-directed RNA polymerase, catalytic domainDomain
IPR022733DPUP/SUD, C-terminal, betacoronavirusDomain
IPR042515Non-structural protein NSP15, N-terminal domain superfamily, coronavirusHomologous Superfamily
IPR043174Non-structural protein NSP15, middle domain superfamilyHomologous Superfamily
IPR044315Nonstructural protein 14, betacoronavirusDomain
IPR038123Non-structural protein NSP4, C-terminal superfamily, coronavirusHomologous Superfamily
IPR042570Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirusHomologous Superfamily
IPR043178Papain-like protease, thumb domain superfamily, coronavirusHomologous Superfamily
IPR046441RNA-dependent RNA polymerase, coronavirusDomain
IPR044863Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domainDomain
IPR044343Nonstructural protein 13, 1B domain, coronavirusDomain
IPR038166Polyprotein cleavage domain PL2pro superfamily, betacoronavirusHomologous Superfamily
IPR037227Endoribonuclease EndoU-likeHomologous Superfamily
IPR027352Nonstructural protein 13, zinc-binding domain, coronavirus-likeDomain
IPR009003Peptidase S1, PA clanHomologous Superfamily
IPR013016Peptidase C16, coronavirusDomain
IPR009466Non-structural protein 14, coronavirusDomain
IPR044357NSP3, first ubiquitin-like (Ubl) domain, coronavirusDomain
IPR046436Nidovirus 3'-5' exoribonuclease domainDomain
IPR047570NSP12, interface domain, coronavirusDomain
IPR018995RNA synthesis protein NSP10, coronavirusDomain
IPR043615Nonstructural protein 2, N-terminal domain, coronavirusDomain
IPR050534Coronaviruses polyprotein 1abFamily
IPR043177Papain-like protease, N-terminal domain superfamily, coronavirusHomologous Superfamily
IPR043606Coronavirus replicase NSP15, N-terminal oligomerizationDomain
IPR044330Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirusDomain
IPR041679DNA2/NAM7 helicase-like, C-terminalDomain
IPR024375Non-structural protein NSP3, SUD-M domain, betacoronavirusDomain
IPR014828Non-structural protein NSP7, coronavirusDomain
IPR043503Papain-like viral protease, palm and finger domains, coronavirusHomologous Superfamily
IPR014829Non-structural protein NSP8, coronavirusDomain
IPR036499Non-structural protein NSP9 superfamily, coronavirusHomologous Superfamily
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
IPR044389Non-structural protein 2, SARS-CoV-likeDomain
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
IPR008740Peptidase C30, coronavirusDomain
IPR036333RNA synthesis protein NSP10 superfamily, coronavirusHomologous Superfamily
IPR047573Non-structural protein 2, middle domain, coronavirusDomain
IPR049894Coronavirus NSP3, 3Ecto domainDomain
IPR043472Macro domain-likeHomologous Superfamily
IPR043609NendoU domain, nidovirusDomain
IPR032592Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirusDomain
IPR043613Non-structural protein 2, C-terminal domain, coronavirusDomain
IPR038083Non-structural protein NSP3A domain-like superfamilyHomologous Superfamily
IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
IPR044351RNA-dependent RNA polymerase, SARS-CoV-likeDomain
IPR024358Non-structural protein NSP3, N-terminal, betacoronavirusDomain
IPR048673Nonstructural protein 13, stalk domain, coronavirusDomain
IPR046435NSP14, guanine-N7-methyltransferase domain, coronavirusDomain
IPR009469RNA-dependent RNA polymerase, N-terminal, coronavirusDomain
IPR043611Coronavirus replicase NSP3, C-terminalDomain
IPR044864Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirusDomain
IPR047566Coronavirus replicase NSP3, Y domainDomain
IPR048672Nonstructural protein 13, zinc-binding domain, coronavirusDomain
IPR043612Non-structural protein NSP4, N-terminal, coronavirusDomain
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
IPR043608Nonstructural protein 15, middle domain, coronavirusDomain
IPR044353NSP3, second ubiquitin-like (Ubl) domain, coronavirusDomain
IPR037204Non-structural protein NSP7 superfamily, coronavirusHomologous Superfamily
IPR046443NSP1, globular domain, alpha/betacoronavirusDomain
IPR043610Non-structural protein 6, coronavirusDomain
IPR027351(+) RNA virus helicase core domainDomain
IPR044322Nonstructural protein 15, middle domain, alpha/betacoronavirusDomain
IPR009461Non-structural protein NSP16, coronavirus-likeDomain
IPR043477Peptidase C30, domain 3, coronavirusHomologous Superfamily
IPR043478Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirusHomologous Superfamily
IPR038400Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirusHomologous Superfamily
IPR046442NSP1, C-terminal domain, betacoronavirusDomain
IPR001205RNA-directed RNA polymerase, C-terminal domainDomain
IPR044401NSP15, NendoU domain, coronavirusDomain
IPR014822Non-structural protein NSP9, coronavirusDomain
IPR038030NSP1 globular domain superfamily, betacoronavirusHomologous Superfamily
IPR021590NSP1, globular domain, betacoronavirusDomain
IPR044367Non-structural protein 6, betacoronavirusDomain
IPR037230Non-structural protein NSP8 superfamily, coronavirusHomologous Superfamily
IPR046440Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domainDomain
IPR032505Non-structural protein NSP4, C-terminal, coronavirusDomain
IPR046438Nidovirus 2-O-methyltransferaseDomain
IPR002589Macro domainDomain
IPR047567Non-structural protein NSP3, group 2-specific marker domain, betacoronavirusDomain
IPR044371Non-structural protein 3, X-domain-likeDomain
IPR007094RNA-directed RNA polymerase, catalytic domainDomain