5VQM | pdb_00005vqm

Clostridium difficile TcdB-GTD bound to PA41 Fab

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
F [auth D]	d5vqmd_	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)
C [auth H]	d5vqmh_	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)
E [auth C]	d5vqmc2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d5vqmc1	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)
B [auth L]	d5vqml2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d5vqml1	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)
D [auth B]	d5vqmb_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Glycosylating toxin catalytic domain-like	automated matches	Clostridium difficile (Clostridioides difficile R20291 ) [TaxId: 645463 ],	SCOPe (2.08)
A	d5vqma_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Glycosylating toxin catalytic domain-like	automated matches	Clostridium difficile (Clostridioides difficile R20291 ) [TaxId: 645463 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Glycosylating toxin catalytic domain-like	8078146	4002384	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotide-diphospho-sugar transferases	8078147	3000077	SCOP2 (2022-06-29)

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_Eps	e5vqmD1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (develop294)
C [auth H]	RuBisCO_large_N	e5vqmH1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: RuBisCO_large_N	ECOD (develop294)
E [auth C]	ATP-synt_Eps	e5vqmC1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (develop294)
B [auth L]	RuBisCO_large_N	e5vqmL1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: RuBisCO_large_N	ECOD (develop294)
D [auth B]	ATP-synt_Eps	e5vqmB1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (develop294)
A	RuBisCO_large_N	e5vqmA1	A: alpha bundles	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: RuBisCO_large_N	ECOD (develop294)

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 (4.3.0)
C [auth H]	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)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth B]	1.20.58.1190	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
D [auth B]	1.10.10.1780	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
A	1.20.58.1190	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	1.10.10.1780	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		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
C [auth H], F [auth D]	PA41 mAb, neutralizing	VH-CH1	Homo sapiens (human)	IGHV1-301, IGHJ101, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
B [auth L], E [auth C]	PA41 mAb, neutralizing	L-KAPPA	Homo sapiens (human)	IGKV3-1101, IGKJ202, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H], F [auth D]	Heavy Chain	IGHV1	-	toxin b	SAbDab (2026-03-20)
B [auth L], E [auth C]	Light Chain	IGKV3	Kappa	toxin b	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth H], F [auth D]	PA41 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
B [auth L], E [auth C]	PA41 FAB LIGHT CHAIN	cation binding ion binding binding metal ion binding small molecule binding	response to stimulus immune response immune system process adaptive immune response	cellular anatomical structure extracellular region cell periphery plasma membrane membrane protein-containing complex immunoglobulin complex
A, D [auth B]	Toxin B	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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