6OQ5
Structure of the full-length Clostridium difficile toxin B in complex with 3 VHHs
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | CW_binding_1 | e6oq5A6 | A: beta duplicates or obligate multimers | X: beta-hairpin stack (From Topology) | H: beta-hairpin stack (From Topology) | T: beta-hairpin stack | F: CW_binding_1 | ECOD (1.6) |
A | TcdA_TcdB_pore_2nd | e6oq5A5 | A: beta duplicates or obligate multimers | X: Toxin A (TcdA) delivery domain (From Topology) | H: Toxin A (TcdA) delivery domain (From Topology) | T: Toxin A (TcdA) delivery domain | F: TcdA_TcdB_pore_2nd | ECOD (1.6) |
A | TcdA_TcdB_pore_1st | e6oq5A4 | A: alpha arrays | X: Toxin A (TcdA) helical domain (From Topology) | H: Toxin A (TcdA) helical domain (From Topology) | T: Toxin A (TcdA) helical domain | F: TcdA_TcdB_pore_1st | ECOD (1.6) |
A | MLD | e6oq5A1 | A: alpha bundles | X: Bromodomain-like | H: PMT helical bundle domain-like | T: PMT helical bundle domain-like | F: MLD | ECOD (1.6) |
A | TcdA_TcdB | e6oq5A2 | A: a/b three-layered sandwiches | X: Nucleotide-diphospho-sugar transferases (From Topology) | H: Nucleotide-diphospho-sugar transferases (From Topology) | T: Nucleotide-diphospho-sugar transferases | F: TcdA_TcdB | ECOD (1.6) |
A | UNK_F_TYPE | e6oq5A3 | A: a/b three-layered sandwiches | X: Caspase-like (From Topology) | H: Caspase-like (From Topology) | T: Caspase-like | F: UNK_F_TYPE | ECOD (1.6) |
B [auth D] | V-set_12 | e6oq5D1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_12 | ECOD (1.6) |
D [auth F] | V-set_8 | e6oq5F1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_8 | ECOD (1.6) |
C [auth E] | V-set_12 | e6oq5E1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_12 | ECOD (1.6) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
B [auth D] | Heavy Chain | IGHV1 | - | toxin b | SAbDab (2024-11-01) |
D [auth F] | Heavy Chain | IGHV1 | - | toxin b | SAbDab (2024-11-01) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF12919 | TcdA/TcdB catalytic glycosyltransferase domain (TcdA_TcdB) | TcdA/TcdB catalytic glycosyltransferase domain | This domain represents the N-terminal glycosyltransferase from a set of toxins found in some bacteria. This domain in TcdB glycosylates the host RhoA protein. | Domain | |
PF12918 | TcdB toxin N-terminal helical domain (TcdB_N) | TcdB toxin N-terminal helical domain | This is a short helical bundle domain found associated with the catalytic domain of the TcdB toxin from C. difficile [1]. The function of this domain is unknown, but it may be involved in substrate recognition. | Domain | |
PF01473 | Putative cell wall binding repeat (Choline_bind_1) | Putative cell wall binding repeat | - | Repeat | |
PF19127 | Choline-binding repeat (Choline_bind_3) | Choline-binding repeat | - | Repeat | |
PF11713 | Peptidase C80 family (Peptidase_C80) | Peptidase C80 family | This family belongs to cysteine peptidase family C80. | Domain | |
PF11647 | Membrane Localization Domain (MLD) | Membrane Localization Domain | This is a membrane localization domain found in multiple families of bacterial toxins including all of the clostridial glucosyltransferase toxins and various MARTX toxins (multifunctional-autoprocessing RTX toxins) [1,4]. In the Pasteurella multocida ... | Domain | |
PF12920 | TcdA/TcdB pore forming domain (TcdA_TcdB_pore) | TcdA/TcdB pore forming domain | - | Family | |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR038383 | CGT/MARTX, cysteine protease (CPD) domain superfamily | Homologous Superfamily | |
IPR024772 | TcdA/TcdB toxin, N-terminal helical domain | Domain | |
IPR020974 | CGT/MARTX, cysteine protease (CPD) domain | Domain | |
IPR024769 | TcdA/TcdB toxin, pore forming domain | Domain | |
IPR029044 | Nucleotide-diphospho-sugar transferases | Homologous Superfamily | |
IPR020972 | Dermonecrotic/RTX toxin, membrane localization domain | Domain | |
IPR024770 | TcdA/TcdB toxin, catalytic glycosyltransferase domain | Domain | |
IPR018337 | Cell wall/choline-binding repeat | Repeat |
Membrane Protein Annotation: OPM OPM Database Homepage
Chains | External Link | Type | Class | Superfamily | Family |
---|---|---|---|---|---|
OPM | Monotopic/peripheral | Alpha/Beta monotopic/peripheral | Nucleotide-diphospho-sugar transferases | Glycosylating toxin |