4YAQ | pdb_00004yaq

Crystal structure of a computationally optimized PG9 mutant

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]	d4yaql2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d4yaql1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d4yaqb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d4yaqb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth H]	d4yaqh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d4yaqa_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(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)
B [auth L]	V-set	e4yaqL1	A: alpha bundles	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: V-set	ECOD (develop294)
D [auth B]	V-set	e4yaqB1	A: alpha bundles	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: V-set	ECOD (develop294)
A [auth H]	V-set	e4yaqH2	A: alpha bundles	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: V-set	ECOD (develop294)
A [auth H]	EF-hand_1, EF-hand_6, EF-hand_7	e4yaqH3	A: alpha bundles	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (develop294)
C [auth A]	V-set	e4yaqA1	A: alpha bundles	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: V-set	ECOD (develop294)
C [auth A]	EF-hand_1, EF-hand_6, EF-hand_7	e4yaqA2	A: alpha bundles	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth B]	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)
C [auth A]	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], D [auth B]	PG9 mAb, anti-gp120 V1-V2 glycon specific [HIV-1], broadly	L-LAMBDA	Homo sapiens (human)	IGLV2-1401, IGLJ101, IGLC3*03	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
A [auth H], C [auth A]	PG9 mAb, anti-gp120 V1-V2 glycon specific [HIV-1], broadly	VH-CH1	Homo sapiens (human)	IGHV3-3002, IGHV3-3003, IGHV3-3006, IGHV3-3012, IGHV3-3019, IGHV3-3301, IGHV3-3304, IGHV3-3305, IGHV3-30-502, IGHJ603, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	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
B [auth L], D [auth B]	Light Chain	IGLV2	Lambda	polysaccharide	SAbDab (2026-03-20)
A [auth H], C [auth A]	Heavy Chain	IGHV3	-	polysaccharide	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth L], D [auth B]	PG9_N100FY Light Chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
A [auth H], C [auth A]	PG9_N100FY Fab heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth L], D [auth B]	IPR003597	Immunoglobulin C1-set	Domain
B [auth L], D [auth B]	IPR050150	Immunoglobulin Variable Light Chain	Family
B [auth L], D [auth B]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth L], D [auth B]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth L], D [auth B]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth L], D [auth B]	IPR003599	Immunoglobulin domain subtype	Domain
B [auth L], D [auth B]	IPR007110	Immunoglobulin-like domain	Domain
B [auth L], D [auth B]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth H], C [auth A]	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], C [auth A]	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.