6O41 | pdb_00006o41

Crystal structure of the unbound PGZL1 germline Fab fragment (PGZL1_gVmDmJ)

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)
I [auth O]	d6o41o1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Immunoglobulin-binding domains	Immunoglobulin-binding domains	Immunoglobulin-binding protein G, different constituent domains	(Streptococcus sp. 'group G ) [TaxId: 1320 ],	SCOPe (2.08)
I [auth O]	d6o41o2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptococcus sp. 'group G ) [TaxId: 1320 ],	SCOPe (2.08)
H [auth N]	d6o41n1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Immunoglobulin-binding domains	Immunoglobulin-binding domains	Immunoglobulin-binding protein G, different constituent domains	(Streptococcus sp. 'group G ) [TaxId: 1320 ],	SCOPe (2.08)
H [auth N]	d6o41n2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptococcus sp. 'group G ) [TaxId: 1320 ],	SCOPe (2.08)
G [auth M]	d6o41m1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Immunoglobulin-binding domains	Immunoglobulin-binding domains	Immunoglobulin-binding protein G, different constituent domains	(Streptococcus sp. 'group G ) [TaxId: 1320 ],	SCOPe (2.08)
G [auth M]	d6o41m2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptococcus sp. 'group G ) [TaxId: 1320 ],	SCOPe (2.08)
E [auth C]	d6o41c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d6o41c2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d6o41a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d6o41a2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth L]	d6o41l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth L]	d6o41l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(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)
F [auth D]	ATP-synt	e6o41D1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (v294.1)
D [auth B]	ATP-synt	e6o41B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (v294.1)
B [auth H]	ATP-synt	e6o41H1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (v294.1)
I [auth O]	ATP-synt	e6o41O1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (v294.1)
H [auth N]	ATP-synt	e6o41N1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (v294.1)
G [auth M]	ATP-synt	e6o41M1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (v294.1)
E [auth C]	ATP-synt	e6o41C1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (v294.1)
C [auth A]	ATP-synt	e6o41A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (v294.1)
A [auth L]	ATP-synt	e6o41L1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: ATP-synt	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
I [auth O]	3.10.20.10	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
H [auth N]	3.10.20.10	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
G [auth M]	3.10.20.10	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
E [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

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]	PGZL1 IGHV1-6906 (100%)/ IGKV3-2001 (98.9%)	VH-CH1	Homo sapiens (human)	IGHV1-6906, IGHV1-6914, IGHJ301, IGHJ302, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG1*11	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202611-0)
A [auth L], C [auth A], E [auth C]	PGZL1 IGHV1-6906 (100%)/ IGKV3-2001 (98.9%)	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ501, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202611-0)

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]	Heavy Chain	IGHV1	-	immunoglobulin g-binding protein g (domain iii)	SAbDab (2026-03-27)
A [auth L], C [auth A], E [auth C]	Light Chain	IGKV3	Kappa	immunoglobulin g-binding protein g (domain iii)	SAbDab (2026-03-27)

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]	germline PGZL1_gVmDmJ heavy chain	-	-	-
G [auth M], H [auth N], I [auth O]	Immunoglobulin G-binding protein G (DOMAIN III)	protein-containing complex binding binding immunoglobulin binding IgG binding	-	-
A [auth L], C [auth A], E [auth C]	germline PGZL1_gVmDmJ light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth M], H [auth N], I [auth O]	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
G [auth M], H [auth N], I [auth O]	IPR005877	YSIRK Gram-positive signal peptide	Domain
G [auth M], H [auth N], I [auth O]	IPR000724	IgG-binding B	Domain
G [auth M], H [auth N], I [auth O]	IPR019950	M protein-type anchor motif	Conserved Site
G [auth M], H [auth N], I [auth O]	IPR035152	GA-like domain	Domain
G [auth M], H [auth N], I [auth O]	IPR019931	LPXTG cell wall anchor motif	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.