3VRL | pdb_00003vrl

Crystal structure of BMJ4 p24 capsid protein in complex with A10F9 Fab

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Retrovirus capsid protein C-terminal domain	8077065	4000865	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Retrovirus capsid dimerization domain-like	8077066	3001819	SCOP2 (2022-06-29)
F [auth D]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077066	3001819	SCOP2B (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	Gag_p24_C	e3vrlC1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
F [auth D]	Gag_p24_C	e3vrlD1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
B [auth L]	C1-set_4	e3vrlL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B [auth L]	V-set	e3vrlL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E [auth F]	C1-set_4	e3vrlF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E [auth F]	V-set	e3vrlF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
A [auth H]	C1-set_1	e3vrlH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
A [auth H]	V-set_12	e3vrlH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
D [auth E]	C1-set_1	e3vrlE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
D [auth E]	V-set_12	e3vrlE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
F [auth D]	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B [auth L], E [auth F]	A10F9 Fab	L-KAPPA	Mus musculus (house mouse)	IGKV12-4102, IGKV12-4101, IGKJ101, IGKJ102, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202546-0)
A [auth H], D [auth E]	A10F9 Fab	VH-CH1	Mus musculus (house mouse)	IGHV5-6-401, IGHJ401, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202546-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L], E [auth F]	Light Chain	IGKV12	Kappa	gag protein	SAbDab (2025-11-28)
A [auth H], D [auth E]	Heavy Chain	IGHV5	-	gag protein	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth L], E [auth F]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
B [auth L], E [auth F]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A [auth H], D [auth E]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A [auth H], D [auth E]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F [auth D]	Gag protein	structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding	viral gene expression viral process viral translational frameshifting viral translation virion assembly viral budding viral budding via host ESCRT complex viral life cycle	host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region membrane virion component virion membrane host cell nucleus host cell plasma membrane host cell membrane viral nucleocapsid viral capsid
B [auth L], E [auth F]	A10F9 Fab light chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
A [auth H], D [auth E]	A10F9 Fab heavy chain	-	response to stimulus immune response immune system process adaptive immune response	protein-containing complex immunoglobulin complex cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F [auth D]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
C, F [auth D]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
C, F [auth D]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
C, F [auth D]	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
C, F [auth D]	IPR001878	Zinc finger, CCHC-type	Domain
C, F [auth D]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
C, F [auth D]	IPR010999	Retroviral matrix protein	Homologous Superfamily
C, F [auth D]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
C, F [auth D]	IPR014817	Gag protein p6	Domain
C, F [auth D]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily
B [auth L], E [auth F]	IPR003597	Immunoglobulin C1-set	Domain
B [auth L], E [auth F]	IPR050150	Immunoglobulin Variable Light Chain	Family
B [auth L], E [auth F]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth L], E [auth F]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth L], E [auth F]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth L], E [auth F]	IPR003599	Immunoglobulin domain subtype	Domain
B [auth L], E [auth F]	IPR007110	Immunoglobulin-like domain	Domain
B [auth L], E [auth F]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A [auth H], D [auth E]	IPR003597	Immunoglobulin C1-set	Domain
A [auth H], D [auth E]	IPR050199	Immunoglobulin Heavy Variable	Family
A [auth H], D [auth E]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth H], D [auth E]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth H], D [auth E]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth H], D [auth E]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth H], D [auth E]	IPR007110	Immunoglobulin-like domain	Domain