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	GP120_2nd	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: GP120_2nd	ECOD (1.6)
A	GP120_3rd	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: GP120_3rd	ECOD (1.6)
A	GP120_1st	e6dcqA1	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)
C	GP120_2nd	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: GP120_2nd	ECOD (1.6)
C	GP120_3rd	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: GP120_3rd	ECOD (1.6)
C	GP120_1st	e6dcqC2	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)
E	GP120_2nd	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: GP120_2nd	ECOD (1.6)
E	GP120_3rd	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: GP120_3rd	ECOD (1.6)
E	GP120_1st	e6dcqE1	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)
B	GP41_1st	e6dcqB1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)
D	GP41_1st	e6dcqD1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)
F	GP41_1st	e6dcqF1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)
G [auth H]	V-set_12	e6dcqH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
I [auth M]	V-set_12	e6dcqM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
H [auth L]	V-set	e6dcqL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
J [auth N]	V-set	e6dcqN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	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 (202436-0)
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 (202436-0)

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 (2024-09-13)
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 (2024-09-13)

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 apoptotic process cell death programmed cell death	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 apoptotic process cell death programmed cell death	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	protein binding binding signaling receptor binding immunoglobulin receptor binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process immune response biological regulation immunoglobulin mediated immune response adaptive immune response immune effector process regulation of response to stimulus immune system process B cell mediated immunity regulation of immune response activation of immune response biological process involved in interspecies interaction between organisms response to other organism defense response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus	extracellular region extracellular space cellular anatomical entity blood microparticle protein-containing complex immunoglobulin complex, circulating immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle extracellular region extracellular space cellular anatomical entity blood microparticle protein-containing complex immunoglobulin complex, circulating immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane
H [auth L], J [auth N]	Immunoglobulin G PGT151 Fab, Light chain	cation binding ion binding binding metal ion binding small molecule binding	response to stimulus immune response immune system process	extracellular region extracellular space 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]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
G [auth H], I [auth M]	IPR050380	Immune Recognition and Response Modulators	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]	IPR013106	Immunoglobulin V-set domain	Domain
G [auth H], I [auth M]	IPR003599	Immunoglobulin domain subtype	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]	IPR050150	Immunoglobulin Variable Light Chain	Family
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]	IPR013106	Immunoglobulin V-set domain	Domain
H [auth L], J [auth N]	IPR003599	Immunoglobulin domain subtype	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