MolNFT v1 · #159464 · protein
Structure of the full-length clostridium difficile toxin B in complex with 3 vhhs
6OQ5: “Structure of the full-length clostridium difficile toxin B in complex with 3 vhhs”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.86). MolNFT v1 #159464 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6OQ5
- Type
- protein
- Length
- 2,695 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin B; 5D; E3; 7F
- UniProt
- M4NKV9
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin B | protein | 2346 | 24% helix, 24% strand | M4NKV9 |
| D | 5D | protein | 126 | 2% helix, 47% strand | — |
| E | E3 | protein | 107 | 3% helix, 44% strand | — |
| F | 7F | protein | 116 | 3% helix, 46% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.86 | 0.88 | 94 | empty |
| 2 | 591 | 0.84 | 0.89 | 76 | empty |
| 3 | 978 | 0.83 | 0.84 | 71 | empty |
| 4 | 105 | 0.76 | 0.95 | 27 | empty |
| 5 | 67 | 0.72 | 0.97 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–D · 891 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 846 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 646 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6OQ5 · Structure of the full-length Clostridium difficile toxin B in complex with 3 VHHs · 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 6OQ5 · PDBe 6OQ5 · UniProt M4NKV9
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