2XV6 | pdb_00002xv6

Crystal structure of the HIV-1 capsid protein C-terminal domain (146- 220) in complex with a camelid VHH.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody 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)
D	d2xv6d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	ALPACA (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
D	d2xv6d2	Artifacts	Tags	Tags	Tags	C-terminal Tags	ALPACA (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
B	d2xv6b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	ALPACA (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
B	d2xv6b2	Artifacts	Tags	Tags	Tags	C-terminal Tags	ALPACA (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
C	d2xv6c_	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	Retrovirus capsid protein C-terminal domain	automated matches	HIV-1 (Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
A	d2xv6a_	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	Retrovirus capsid protein C-terminal domain	automated matches	HIV-1 (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	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8037182	3001819	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8037182	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)
D	PNP_UDP_1	e2xv6D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: PNP_UDP_1	ECOD (v294.1)
B	PNP_UDP_1	e2xv6B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: PNP_UDP_1	ECOD (v294.1)
C	PNP_UDP_1	e2xv6C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: PNP_UDP_1	ECOD (v294.1)
A	PNP_UDP_1	e2xv6A1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: PNP_UDP_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D	Heavy Chain	IGHV1	-	capsid protein p24	SAbDab (2026-04-10)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	CAMELID VHH 9	-	-	-
A, C	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 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, 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 symbiont entry into host cell viral process symbiont entry into host viral life cycle 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 symbiont entry into host cell viral process symbiont entry into host viral life cycle viral genome integration into host DNA viral penetration into host nucleus intracellular transport of virus transport of virus nucleobase-containing compound metabolic process metabolic process cellular 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 viral gene expression viral translational frameshifting viral translation DNA recombination symbiont-mediated activation of host programmed cell death symbiont-mediated activation of host apoptosis symbiont-mediated perturbation of host programmed cell death disruption of cell in another organism 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 proteolysis protein metabolic process	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 viral nucleocapsid 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 viral nucleocapsid viral capsid virion component host cell plasma membrane host cell membrane host cell virion membrane host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

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