4YC2 | pdb_00004yc2

Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 from E. coli in complex with the antibody A32.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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)
F [auth C]	d4yc2c2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth C]	d4yc2c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d4yc2l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d4yc2l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d4yc2h1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d4yc2h2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d4yc2b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d4yc2b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth C]	LRR_1+LRR_8+LRR_14	e4yc2C1	A: alpha bundles	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase	T: Nucleotidyltransferase	F: LRR_1+LRR_8+LRR_14	ECOD (develop294)
C [auth L]	LRR_1+LRR_8+LRR_14	e4yc2L1	A: alpha bundles	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase	T: Nucleotidyltransferase	F: LRR_1+LRR_8+LRR_14	ECOD (develop294)
B [auth H]	LRR_1+LRR_8+LRR_14	e4yc2H1	A: alpha bundles	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase	T: Nucleotidyltransferase	F: LRR_1+LRR_8+LRR_14	ECOD (develop294)
E [auth B]	LRR_1+LRR_8+LRR_14	e4yc2B1	A: alpha bundles	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase	T: Nucleotidyltransferase	F: LRR_1+LRR_8+LRR_14	ECOD (develop294)
A [auth G]	Pre-SET	e4yc2G1	A: alpha bundles	X: alpha/beta knot	H: alpha/beta knot	T: alpha/beta knot	F: Pre-SET	ECOD (develop294)
D [auth A]	Pre-SET	e4yc2A1	A: alpha bundles	X: alpha/beta knot	H: alpha/beta knot	T: alpha/beta knot	F: Pre-SET	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth B]	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], F [auth C]	A32 Fab	L-LAMBDA	Homo sapiens (human)	IGLV2-801, IGLJ201, IGLJ302, IGLJ301, IGLC201, IGLC202, IGLC3*04	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
B [auth H], E [auth B]	A32 Fab	VH-CH1	Homo sapiens (human)	IGHV4-30-401, IGHV4-3102, IGHV4-3103, IGHJ302, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L], F [auth C]	Light Chain	IGLV2	Lambda	the stabilized inner domain of clade a/e hiv-1 gp120 frome. coli	SAbDab (2026-03-20)
B [auth H], E [auth B]	Heavy Chain	IGHV4	-	the stabilized inner domain of clade a/e hiv-1 gp120 frome. coli	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth L], F [auth C]	The antibody A32 Fab light chain.	-	-	-
B [auth H], E [auth B]	The antibody A32 Fab heavy chain.	-	-	-
A [auth G], D [auth A]	The stabilized inner domain of clade A/E HIV-1 gp120 from E. coli	-	viral process membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	virion component viral membrane viral envelope virion membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G], D [auth A]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A [auth G], D [auth A]	IPR036377	Gp120 core superfamily	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.