5F6J | pdb_00005f6j

Crystal Structure of Tier 2 Neutralizing Antibody DH427 from a Rhesus Macaque in Complex with HIV-1 gp120 Core

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth E]	SCOP2B Superfamily	gp120 core	8100784	3001390	SCOP2B (2022-06-29)
A [auth G]	SCOP2B Superfamily	gp120 core	8100784	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)
B [auth E]	Ribosomal_S5_C	e5f6jE1	A: alpha bundles	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: Ribosomal_S5_C	ECOD (develop294)
A [auth G]	Ribosomal_S5_C	e5f6jG1	A: alpha bundles	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: Ribosomal_S5_C	ECOD (develop294)
D [auth B]	DEAD, DEAD_2	e5f6jB1	A: alpha bundles	X: ACP-like	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: DEAD, DEAD_2	ECOD (develop294)
D [auth B]	NTP_transferase	e5f6jB2	A: alpha bundles	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: NTP_transferase	ECOD (develop294)
F [auth H]	DEAD, DEAD_2	e5f6jH2	A: alpha bundles	X: ACP-like	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: DEAD, DEAD_2	ECOD (develop294)
F [auth H]	NTP_transferase	e5f6jH1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: NTP_transferase	ECOD (develop294)
C [auth A]	DEAD, DEAD_2	e5f6jA1	A: alpha bundles	X: ACP-like	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: DEAD, DEAD_2	ECOD (develop294)
E [auth F]	DEAD, DEAD_2	e5f6jF1	A: alpha bundles	X: ACP-like	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: DEAD, DEAD_2	ECOD (develop294)

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
D [auth B], F [auth H]	DH427	VH-CH1	Homo sapiens (human)	IGHV3-2304, IGHJ401, IGHJ402, IGHJ403, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
C [auth A], E [auth F]	DH427	L-LAMBDA	Homo sapiens (human)	IGLV2-801, IGLV2-802, IGLJ101, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	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
D [auth B], F [auth H]	Heavy Chain	IGHV3	-	envelope glycoprotein gp120 of hiv-1 clade c	SAbDab (2026-03-20)
C [auth A], E [auth F]	Light Chain	IGLV2	Lambda	envelope glycoprotein gp120 of hiv-1 clade c	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G], B [auth E]	ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C	-	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host	virion component viral membrane viral envelope virion membrane
D [auth B], F [auth H]	DH427 Antibody Heavy Chain	-	-	-
C [auth A], E [auth F]	DH427 Antibody Light Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G], B [auth E]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A [auth G], B [auth E]	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.