7H0A

Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0008485-001


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2B SuperfamilyMacro domain-like8092463 3000458 SCOP2B (2021-05-27)
ASCOP2B SuperfamilyMacro domain-like8092463 3000458 SCOP2B (2021-05-27)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF01661Macro domain (Macro)Macro domainThe Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently ...The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently [2]; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein [3]. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein [4]. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site [5].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B
Papain-like protease nsp3

InterPro: Protein Family Classification InterPro Database Homepage

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