MolNFT v1 · #159466 · protein
Structure of the gtd domain of clostridium difficile toxin B in complex with vhh E3
6OQ7: “Structure of the gtd domain of clostridium difficile toxin B in complex with vhh E3”. X-ray diffraction, 4 ligands (UDP, GLC, MN), 2 pockets (best druggability 0.74). MolNFT v1 #159466 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6OQ7
- Type
- protein
- Length
- 650 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin B; E3
- UniProt
- M4NKV9
- Ligands
- UDP, GLC, MN, MG
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin B | protein | 541 | 59% helix, 8% strand | M4NKV9 |
| C | E3 | protein | 109 | 3% helix, 48% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- MN · Manganese (II) ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.74 | 0.79 | 74 | UDP, GLC, MN, MG |
| 2 | 69 | 0.39 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 734 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6OQ7 · Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH E3 · 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 6OQ7 · PDBe 6OQ7 · UniProt M4NKV9
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