4DQO | pdb_00004dqo

Crystal Structure of PG16 Fab in Complex with V1V2 Region from HIV-1 strain ZM109

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth L]	d4dqol2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d4dqol1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth H]	d4dqoh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	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)
C		e4dqoC1	A: Inserted helical domain in fatty acid synthase subunit beta	X: Voltage-gated ion channels	H: Voltage-gated ion channels	T: FAN1_HTH	F:	ECOD (20:10:01)
B [auth L]		e4dqoL1	A: Alpha-beta plaits	X: Family B DNA polymerase insertion domain	H: Family B DNA polymerase insertion domain	T: Sushi	F:	ECOD (20:10:01)
A [auth H]		e4dqoH1	A: Alpha-beta plaits	X: Family B DNA polymerase insertion domain	H: Family B DNA polymerase insertion domain	T: Sushi	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.10.20.10	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth H]	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
B [auth L]	PG16 mAb, anti-gp120 V1-V2 glycon specific [HIV-1], broadly	L-LAMBDA	Homo sapiens (human)	IGLV2-1401, IGLJ101, IGLJ201, IGLJ302, IGLJ601, IGLJ301, IGLC3*03	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202609-0)
A [auth H]	PG16 mAb, anti-gp120 V1-V2 glycon specific [HIV-1], broadly	VH-CH1	Homo sapiens (human)	IGHV3-3003, IGHV3-3006, IGHV3-3012, IGHV3-3015, IGHV3-3019, IGHV3-3305, IGHJ301, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L]	Light Chain	IGLV2	Lambda	1fd6-v1v2 scaffold zm109 hiv-1 strain	SAbDab (2026-03-13)
A [auth H]	Heavy Chain	IGHV3	-	1fd6-v1v2 scaffold zm109 hiv-1 strain	SAbDab (2026-03-13)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	1FD6-V1V2 scaffold ZM109 HIV-1 strain	structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization positive regulation of receptor clustering biological regulation positive regulation of biological process positive regulation of protein localization to membrane localization within membrane protein localization to membrane localization regulation of cellular localization macromolecule localization receptor clustering positive regulation of protein localization intracellular protein localization regulation of receptor clustering regulation of protein localization to membrane positive regulation of cellular process 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 plasma membrane raft distribution regulation of cellular component organization positive regulation of cellular component organization plasma membrane raft polarization plasma membrane organization membrane raft organization endomembrane system organization membrane raft distribution plasma membrane raft localization membrane raft polarization regulation of plasma membrane raft polarization membrane raft localization regulation of plasma membrane organization positive regulation of plasma membrane raft polarization import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral protein processing symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation of process of another organism	cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region viral membrane viral envelope host cell plasma membrane
B [auth L]	PG16 Fab Light Chain	-	-	-
A [auth H]	PG16 Fab Heavy Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
C	IPR036377	Gp120 core superfamily	Homologous Superfamily
C	IPR000328	Retroviral envelope protein GP41-like	Domain
C	IPR037527	Envelope glycoprotein Gp160	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth H]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420
A [auth H]	TYS	Parent Component: TYR RESID: AA0031 , AA0172 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420 , O4'-sulfo-L-tyrosine MOD:00181

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.