2XT1 | pdb_00002xt1

Crystal structure of the HIV-1 capsid protein C-terminal domain (146- 231) 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
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)
B	d2xt1b1	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	d2xt1b2	Artifacts	Tags	Tags	Tags	C-terminal Tags	ALPACA (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
A	d2xt1a_	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)
A	SCOP2 Family	Retrovirus capsid protein C-terminal domain	8101662	4000865	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Retrovirus capsid dimerization domain-like	8101663	3001819	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)
B	V-set_8	e2xt1B1	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)
A	Gag_p24_C	e2xt1A1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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)

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	CAMELID VHH 9	VH	Vicugna pacos (alpaca)	IGHV3S401, IGHJ401	V-DOMAIN VH	IG	(VH)	IMGT (202547-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV1	-	gag polyprotein	SAbDab (2025-12-05)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	CAMELID VHH 9	-	-	-
A	GAG POLYPROTEIN	RNA binding binding nucleic acid binding	viral gene expression viral process viral translational frameshifting viral translation	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle membrane host cell plasma membrane host cell membrane viral nucleocapsid viral capsid host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle membrane host cell plasma membrane host cell membrane viral nucleocapsid viral capsid virion component host cell cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.