6DCQ

Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
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)
G [auth H]	d6dcqh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I [auth M]	d6dcqm_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth L]	d6dcql_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J [auth N]	d6dcqn_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (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)
A	PF00516	e6dcqA3	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: PF00516	ECOD (1.6)
A	PF00516	e6dcqA2	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: PF00516	ECOD (1.6)
A	PF00516	e6dcqA1	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: PF00516	ECOD (1.6)
C	PF00516	e6dcqC3	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: PF00516	ECOD (1.6)
C	PF00516	e6dcqC1	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: PF00516	ECOD (1.6)
C	PF00516	e6dcqC2	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: PF00516	ECOD (1.6)
E	PF00516	e6dcqE3	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: PF00516	ECOD (1.6)
E	PF00516	e6dcqE2	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: PF00516	ECOD (1.6)
E	PF00516	e6dcqE1	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: PF00516	ECOD (1.6)
B	PF00517	e6dcqB1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: PF00517	ECOD (1.6)
D	PF00517	e6dcqD1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: PF00517	ECOD (1.6)
F	PF00517	e6dcqF1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: PF00517	ECOD (1.6)
G [auth H]	PF07686	e6dcqH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I [auth M]	PF07686	e6dcqM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H [auth L]	PF07686	e6dcqL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
J [auth N]	PF07686	e6dcqN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

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
G [auth H], I [auth M]	Fab PGT151	VH-CH1	Homo sapiens (human)	IGHV3-3001, IGHV3-3003, IGHV3-3004, IGHV3-3006, IGHV3-3007, IGHV3-3009, IGHV3-3010, IGHV3-3011, IGHV3-3012, IGHV3-3014, IGHV3-3016, IGHV3-3017, IGHV3-3019, IGHV3-30-301, IGHV3-3305, IGHV3-30-303, IGHJ301, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
H [auth L], J [auth N]	Fab PGT151	L-KAPPA	Homo sapiens (human)	IGKV2D-2902, IGKJ401, IGKJ402, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G [auth H], I [auth M]	Heavy Chain	IGHV3	-	envelope glycoprotein gp160 \| envelope glycoprotein gp160, envelope glycoprotein gp160 \| envelope glycoprotein gp160 \| envelope glycoprotein gp160	SAbDab (2024-04-26)
H [auth L], J [auth N]	Light Chain	IGKV2	Kappa	envelope glycoprotein gp160 \| envelope glycoprotein gp160, envelope glycoprotein gp160 \| envelope glycoprotein gp160 \| envelope glycoprotein gp160	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF00516	Envelope glycoprotein GP120 (GP120)	Envelope glycoprotein GP120	-	Family
B, D, F	PF00517	Retroviral envelope protein (GP41)	Retroviral envelope protein	-	Family
G [auth H], I [auth M]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
H [auth L], J [auth N]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	Envelope glycoprotein gp160	structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response biological process involved in interaction with host response to biotic stimulus viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction modulation by symbiont of host process response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host cellular process import into cell receptor-mediated endocytosis of virus by host cell transport viral life cycle establishment of localization vesicle-mediated transport 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 transport of virus	virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region cell periphery plasma membrane membrane viral membrane viral envelope host cell plasma membrane
B, D, F	Envelope glycoprotein gp160	structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response biological process involved in interaction with host response to biotic stimulus viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction modulation by symbiont of host process response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host cellular process import into cell receptor-mediated endocytosis of virus by host cell transport viral life cycle establishment of localization vesicle-mediated transport 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 transport of virus	virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region cell periphery plasma membrane membrane viral membrane viral envelope host cell plasma membrane
G [auth H], I [auth M]	Immunoglobulin G PGT151 Fab, Heavy chain	-	-	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex
H [auth L], J [auth N]	Immunoglobulin G PGT151 Fab, Light chain	-	-	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A, C, E	IPR036377	Gp120 core superfamily	Homologous Superfamily
A, C, E	IPR000328	Retroviral envelope protein GP41-like	Domain
A, C, E	IPR037527	Envelope glycoprotein Gp160	Family
B, D, F	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
B, D, F	IPR036377	Gp120 core superfamily	Homologous Superfamily
B, D, F	IPR000328	Retroviral envelope protein GP41-like	Domain
B, D, F	IPR037527	Envelope glycoprotein Gp160	Family
G [auth H], I [auth M]	IPR003597	Immunoglobulin C1-set	Domain
G [auth H], I [auth M]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
G [auth H], I [auth M]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
G [auth H], I [auth M]	IPR003599	Immunoglobulin subtype	Domain
G [auth H], I [auth M]	IPR013106	Immunoglobulin V-set domain	Domain
G [auth H], I [auth M]	IPR007110	Immunoglobulin-like domain	Domain
G [auth H], I [auth M]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
H [auth L], J [auth N]	IPR003597	Immunoglobulin C1-set	Domain
H [auth L], J [auth N]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
H [auth L], J [auth N]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
H [auth L], J [auth N]	IPR003599	Immunoglobulin subtype	Domain
H [auth L], J [auth N]	IPR013106	Immunoglobulin V-set domain	Domain
H [auth L], J [auth N]	IPR007110	Immunoglobulin-like domain	Domain
H [auth L], J [auth N]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site