2GOL

Xray Structure of Gag278

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth D]	d2gold_	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	HIV-1 capsid protein	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
B	d2golb_	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	HIV-1 capsid protein	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
A	d2gola_	All alpha proteins	Retroviral matrix proteins	Retroviral matrix proteins	Immunodeficiency virus matrix proteins	HIV-1 matrix protein (HIV-1 MA, HIVp17, p17, MA)	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth D]	SCOP2 Family	Retrovirus capsid protein N-terminal core domain	8101630	4001095	SCOP2 (2022-06-29)
C [auth D]	SCOP2 Superfamily	Retrovirus capsid protein N-terminal core domain	8101631	3000745	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Retrovirus capsid protein N-terminal core domain	8101631	3000745	SCOP2B (2022-06-29)
A	SCOP2 Family	Immunodeficiency virus matrix proteins	8029601	4001043	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Retroviral matrix proteins	8041980	3000562	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth D]	PF00607	e2golD1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: PF00607	ECOD (1.6)
B	PF00607	e2golB1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: PF00607	ECOD (1.6)
A	PF00540	e2golA1	A: alpha arrays	X: Retroviral matrix proteins (From Topology)	H: Retroviral matrix proteins (From Topology)	T: Retroviral matrix proteins	F: PF00540	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth D]	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
B	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
A	1.10.150.90	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, C [auth D]	PF00607	gag protein p24 N-terminal domain (Gag_p24)	gag protein p24 N-terminal domain	p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.	Domain
B, C [auth D]	PF19317	Gag protein p24 C-terminal domain (Gag_p24_C)	Gag protein p24 C-terminal domain	p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.	Domain
A	PF00540	gag gene protein p17 (matrix protein) (Gag_p17)	gag gene protein p17 (matrix protein)	The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, C [auth D]	Capsid protein p24 (CA)	-	viral process	viral capsid virion component
A	Matrix protein p17 (MA)	structural molecule activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, C [auth D]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
B, C [auth D]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
B, C [auth D]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily
A	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A	IPR010999	Retroviral matrix protein	Homologous Superfamily
A	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.