4FQQ | pdb_00004fqq

Crystal Structure of Germline Antibody PGT121-GL Fab

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H [auth F]	d4fqqf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth F]	d4fqqf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth D]	d4fqqd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth D]	d4fqqd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d4fqqb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d4fqqb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d4fqqh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d4fqqh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth E]	d4fqqe1	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)
G [auth E]	d4fqqe2	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)
E [auth C]	d4fqqc1	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)
E [auth C]	d4fqqc2	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)
C [auth A]	d4fqqa1	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)
C [auth A]	d4fqqa2	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)
A [auth L]	d4fqql1	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)
A [auth L]	d4fqql2	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H [auth F]	V-set	e4fqqF3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (develop294)
F [auth D]	V-set	e4fqqD3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (develop294)
D [auth B]	SmpA_OmlA	e4fqqB1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (develop294)
B [auth H]	PK_Tyr_Ser-Thr	e4fqqH1	A: alpha bundles	X: Globin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: PK_Tyr_Ser-Thr	ECOD (develop294)
G [auth E]	RRM_1	e4fqqE1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (develop294)
E [auth C]	RRM_1	e4fqqC1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (develop294)
C [auth A]	Ig_2	e4fqqA3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ig_2	ECOD (develop294)
A [auth L]	PK_Tyr_Ser-Thr	e4fqqL1	A: alpha bundles	X: Globin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: PK_Tyr_Ser-Thr	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth D]	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)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth C]	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)
A [auth L]	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 H], D [auth B], F [auth D], H [auth F]	Antibody Fab Fragment	VH-CH1	Homo sapiens (human)	IGHV4-5901, IGHV4-5903, IGHV4-5908, IGHJ603, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
A [auth L], C [auth A], E [auth C], G [auth E]	Antibody Fab Fragment	L-LAMBDA	Homo sapiens (human)	IGLV3-2102, IGLJ201, IGLJ302, IGLJ301, IGLC201, IGLC202, IGLC3*04	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
B [auth H], D [auth B], F [auth D], H [auth F]	Heavy Chain	IGHV4	-	-	SAbDab (2026-03-20)
A [auth L], C [auth A], E [auth C], G [auth E]	Light Chain	IGLV3	Lambda	-	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth H], D [auth B], F [auth D], H [auth F]	Fab heavy 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 L], C [auth A], E [auth C], G [auth E]	Fab 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth H], D [auth B], F [auth D], H [auth F]	IPR003597	Immunoglobulin C1-set	Domain
B [auth H], D [auth B], F [auth D], H [auth F]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth H], D [auth B], F [auth D], H [auth F]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth H], D [auth B], F [auth D], H [auth F]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth H], D [auth B], F [auth D], H [auth F]	IPR003599	Immunoglobulin domain subtype	Domain
B [auth H], D [auth B], F [auth D], H [auth F]	IPR007110	Immunoglobulin-like domain	Domain
B [auth H], D [auth B], F [auth D], H [auth F]	IPR050380	Immune Recognition and Response Modulators	Family
B [auth H], D [auth B], F [auth D], H [auth F]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A [auth L], C [auth A], E [auth C], G [auth E]	IPR003597	Immunoglobulin C1-set	Domain
A [auth L], C [auth A], E [auth C], G [auth E]	IPR050150	Immunoglobulin Variable Light Chain	Family
A [auth L], C [auth A], E [auth C], G [auth E]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth L], C [auth A], E [auth C], G [auth E]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth L], C [auth A], E [auth C], G [auth E]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth L], C [auth A], E [auth C], G [auth E]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth L], C [auth A], E [auth C], G [auth E]	IPR007110	Immunoglobulin-like domain	Domain
A [auth L], C [auth A], E [auth C], G [auth E]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

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.