5F9W | pdb_00005f9w

Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-directed antibody CH235 in complex with HIV-1 clade A/E 93TH057 gp120

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
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 L]	d5f9wl2	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 L]	d5f9wl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5f9wc2	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	d5f9wc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth H]	d5f9wh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5f9wb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth G]	SCOP2B Superfamily	gp120 core	8096276	3001390	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	gp120 core	8096276	3001390	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)
F [auth L]	Como_SCP	e5f9wL1	A: alpha bundles	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: Como_SCP	ECOD (develop294)
C	Como_SCP	e5f9wC1	A: alpha bundles	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: Como_SCP	ECOD (develop294)
E [auth H]	Como_SCP	e5f9wH1	A: alpha bundles	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: Como_SCP	ECOD (develop294)
B	Como_SCP	e5f9wB1	A: alpha bundles	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: Como_SCP	ECOD (develop294)
D [auth G]	AWS	e5f9wG1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: AWS	ECOD (develop294)
A	AWS	e5f9wA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: AWS	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth H]	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)
D [auth G]	2.170.40.20	Mainly Beta	Beta Complex	HIV Envelope Protein Gp120	Chain G	CATH (4.3.0)
A	2.170.40.20	Mainly Beta	Beta Complex	HIV Envelope Protein Gp120	Chain G	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, F [auth L]	CH235 mAb, [HIV-1], broadly neutralizing	L-KAPPA	Homo sapiens (human)	IGKV3-1501, IGKV3D-1501, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
B, E [auth H]	CH235 mAb, [HIV-1], broadly neutralizing	VH-CH1	Homo sapiens (human)	IGHV1-4601, IGHV1-4603, IGHJ401, IGHJ402, IGHJ403, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, F [auth L]	Light Chain	IGKV3	Kappa	clade a/e 93th057 hiv-1 gp120 core	SAbDab (2026-03-20)
B, E [auth H]	Heavy Chain	IGHV1	-	clade a/e 93th057 hiv-1 gp120 core	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F [auth L]	Light chain of CH235-lineage antibody CH235	-	-	-
B, E [auth H]	Heavy chain of CH235-lineage antibody CH235	-	-	-
A, D [auth G]	clade A/E 93TH057 HIV-1 gp120 core	-	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, D [auth G]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A, D [auth G]	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.