1E6J | pdb_00001e6j

Crystal structure of HIV-1 capsid protein (p24) in complex with Fab13B5

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth P]	d1e6jp1	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	Retrovirus capsid protein C-terminal domain	HIV capsid protein, dimerisation domain	(HIV-1 M:B_HXB2R ) [TaxId: 11706 ],	SCOPe (2.08)
C [auth P]	d1e6jp2	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	(HIV-1 M:B_HXB2R ) [TaxId: 11706 ],	SCOPe (2.08)
B [auth L]	d1e6jl1	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)
B [auth L]	d1e6jl2	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)
A [auth H]	d1e6jh1	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)
A [auth H]	d1e6jh2	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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth P]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	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 [auth P]	Gag_p24_C	e1e6jP1	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)
C [auth P]	Gag_p24_N	e1e6jP2	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)
B [auth L]	C1-set_4	e1e6jL2	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	e1e6jL1	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	e1e6jH2	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_10	e1e6jH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth P]	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 P]	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)
A [auth H]	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]	13B5 mAb, anti-p24 [HIV-1]	L-KAPPA	Mus musculus (house mouse)	IGKV4-8601, IGKJ203, IGKJ401, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202538-0)
A [auth H]	13B5 mAb, anti-p24 [HIV-1]	VH-CH1	Mus musculus (house mouse)	IGHV1-401, IGHJ201, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202538-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L]	Light Chain	IGKV4	Kappa	capsid protein p24	SAbDab (2025-10-03)
A [auth H]	Heavy Chain	IGHV1	-	capsid protein p24	SAbDab (2025-10-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth P]	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 [auth H]	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]	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 [auth P]	CAPSID PROTEIN P24	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 hydrolase activity, acting on ester bonds nuclease activity exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity 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 hydrolase activity, acting on ester bonds nuclease activity 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 nucleic acid binding RNA-directed DNA polymerase activity RNA binding RNA stem-loop binding identical protein binding protein binding peptidase activity catalytic activity, acting on a protein integrase activity aspartic-type peptidase activity aspartic-type endopeptidase activity endopeptidase activity lipid binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism RNA-DNA hybrid ribonuclease activity RNA endonuclease activity structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction viral process viral life cycle symbiont entry into host cell symbiont entry into host viral genome integration into host DNA viral penetration into host nucleus symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction viral process viral life cycle symbiont entry into host cell symbiont entry into host viral genome integration into host DNA viral penetration into host nucleus intracellular transport of virus transport of virus establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process nucleobase-containing compound metabolic process DNA recombination DNA metabolic process nucleic acid metabolic process regulation of biological process symbiont-mediated activation of host programmed cell death regulation of cellular process symbiont-mediated activation of host apoptosis symbiont-mediated perturbation of host programmed cell death biological regulation regulation of killing of cells of another organism disruption of cell in another organism regulation of cell killing symbiont-mediated perturbation of host apoptosis disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing	cellular anatomical structure 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 host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region cellular anatomical structure 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 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 host cell virion membrane host cell nucleus
B [auth L]	IMMUNOGLOBULIN	-	-	-
A [auth H]	IMMUNOGLOBULIN	cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth P]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C [auth P]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
C [auth P]	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
C [auth P]	IPR001878	Zinc finger, CCHC-type	Domain
C [auth P]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
C [auth P]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
C [auth P]	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
C [auth P]	IPR018061	Retropepsins	Domain
C [auth P]	IPR010661	Reverse transcriptase thumb	Domain
C [auth P]	IPR002156	Ribonuclease H domain	Domain
C [auth P]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
C [auth P]	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
C [auth P]	IPR001584	Integrase, catalytic core	Domain
C [auth P]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
C [auth P]	IPR010999	Retroviral matrix protein	Homologous Superfamily
C [auth P]	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
C [auth P]	IPR001969	Aspartic peptidase, active site	Active Site
C [auth P]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
C [auth P]	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
C [auth P]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
C [auth P]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C [auth P]	IPR001037	Integrase, C-terminal, retroviral	Domain
C [auth P]	IPR034170	Retropepsin-like catalytic domain	Domain
C [auth P]	IPR000477	Reverse transcriptase domain	Domain
C [auth P]	IPR010659	Reverse transcriptase connection	Domain
C [auth P]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily
A [auth H]	IPR003597	Immunoglobulin C1-set	Domain
A [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth H]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth H]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth H]	IPR007110	Immunoglobulin-like domain	Domain
A [auth H]	IPR050380	Immune Recognition and Response Modulators	Family