Annotations: 1AFV

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1afvb_	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	d1afva_	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)
C [auth L]	d1afvl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d1afvl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth M]	d1afvm1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth M]	d1afvm2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth H]	d1afvh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth H]	d1afvh2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth K]	d1afvk1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth K]	d1afvk2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Gag_p24_N	e1afvB1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
A	Gag_p24_N	e1afvA1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
C [auth L]	C1-set_4	e1afvL2	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)
C [auth L]	V-set	e1afvL1	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 M]	C1-set_4	e1afvM2	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 M]	V-set	e1afvM1	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)
D [auth H]	V-set_8	e1afvH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
D [auth H]	C1-set_1	e1afvH2	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)
F [auth K]	V-set_8	e1afvK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
F [auth K]	C1-set_1	e1afvK2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth K]	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
C [auth L], E [auth M]	25.3 mAb, anti-p24 [HIV-1]	L-KAPPA	Mus musculus (house mouse)	IGKV3-201, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
D [auth H], F [auth K]	25.3 mAb, anti-p24 [HIV-1]	VH-CH1	Mus musculus (house mouse)	IGHV1S13001, IGHJ201, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L], E [auth M]	Light Chain	IGKV3	Kappa	human immunodeficiency virus type 1 capsidprotein	SAbDab (2024-04-19)
D [auth H], F [auth K]	Heavy Chain	IGHV1	-	human immunodeficiency virus type 1 capsidprotein	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
D [auth H], F [auth K]	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
D [auth H], F [auth K]	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
A, B	HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 CAPSID PROTEIN	catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding RNA-directed DNA polymerase activity RNA binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein aspartic-type endopeptidase activity endopeptidase activity lipid binding endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters RNA-DNA hybrid ribonuclease activity RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	viral genome integration into host DNA viral process viral life cycle viral penetration into host nucleus intracellular transport of virus transport of virus biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process viral genome integration into host DNA viral process viral life cycle viral penetration into host nucleus intracellular transport of virus transport of virus biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process DNA integration nucleic acid metabolic process establishment of integrated proviral latency viral latency establishment of viral latency DNA recombination symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism organonitrogen compound metabolic process proteolysis protein metabolic process	membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid viral capsid virion component host cell plasma membrane host cell membrane virion membrane host cell nucleus
C [auth L], E [auth M]	ANTIBODY FAB25.3 FRAGMENT (LIGHT CHAIN)	-	-	-
D [auth H], F [auth K]	ANTIBODY FAB25.3 FRAGMENT (HEAVY CHAIN)	cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B	IPR001878	Zinc finger, CCHC-type	Domain
A, B	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A, B	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B	IPR018061	Retropepsins	Domain
A, B	IPR010661	Reverse transcriptase thumb	Domain
A, B	IPR002156	Ribonuclease H domain	Domain
A, B	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B	IPR001584	Integrase, catalytic core	Domain
A, B	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B	IPR001969	Aspartic peptidase, active site	Active Site
A, B	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A, B	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B	IPR034170	Retropepsin-like catalytic domain	Domain
A, B	IPR000477	Reverse transcriptase domain	Domain
A, B	IPR010659	Reverse transcriptase connection	Domain
A, B	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily
D [auth H], F [auth K]	IPR003597	Immunoglobulin C1-set	Domain
D [auth H], F [auth K]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth H], F [auth K]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth H], F [auth K]	IPR003599	Immunoglobulin subtype	Domain
D [auth H], F [auth K]	IPR013106	Immunoglobulin V-set domain	Domain
D [auth H], F [auth K]	IPR007110	Immunoglobulin-like domain	Domain