MolNFT v1 · #137503 · protein
Clostridium difficile tcdb-gtd bound to PA41 Fab
5VQM · Toxin B: “Clostridium difficile tcdb-gtd bound to PA41 Fab”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #137503 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VQM
- Type
- protein
- Length
- 1,916 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin B; PA41 Fab light chain; PA41 Fab heavy chain
- UniProt
- C9YJ35, Q8TCD0, S6B291
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toxin B | protein | 528 | 56% helix, 8% strand | C9YJ35 |
| L, C | PA41 Fab light chain | protein | 214 | 6% helix, 49% strand | Q8TCD0 |
| H, D | PA41 Fab heavy chain | protein | 216 | 3% helix, 44% strand | S6B291 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.84 | 0.86 | 118 | empty |
| 2 | 618 | 0.82 | 0.88 | 72 | empty |
| 3 | 408 | 0.76 | 0.85 | 43 | empty |
| 4 | 534 | 0.76 | 0.83 | 46 | empty |
| 5 | 175 | 0.65 | 0.86 | 32 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1911 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 1793 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 623 Ų buried · 4 hydrogen bonds · protein-protein
- H–B · 531 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 502 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5VQM · Clostridium difficile TcdB-GTD bound to PA41 Fab · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt C9YJ35
- Every structure of UniProt Q8TCD0
- Every structure of UniProt S6B291
- Elsewhere: RCSB PDB 5VQM · PDBe 5VQM · UniProt C9YJ35 · UniProt Q8TCD0 · UniProt S6B291
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