MolNFT v1 · #159465 · protein
Structure of the pore forming fragment of clostridium difficile toxin B in complex with vhh 5D
6OQ6: “Structure of the pore forming fragment of clostridium difficile toxin B in complex with vhh 5D”. X-ray diffraction, 3 pockets (best druggability 0.53). MolNFT v1 #159465 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OQ6
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin B; 5D
- UniProt
- M4NKV9
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin B | protein | 342 | 11% helix, 44% strand | M4NKV9 |
| D | 5D | protein | 128 | 2% helix, 51% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.53 | 0.76 | 30 | empty |
| 2 | 79 | 0.37 | 0.77 | 22 | empty |
| 3 | 79 | 0.37 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–D · 918 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6OQ6 · Structure of the pore forming fragment of Clostridium difficile toxin B in complex with… · 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 M4NKV9
- Elsewhere: RCSB PDB 6OQ6 · PDBe 6OQ6 · UniProt M4NKV9
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