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Structure of the gtd domain of clostridium difficile toxin B in complex with vhh 7F
Analyse Structure of the gtd domain of clostridium difficile toxin B in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OQ8
- Type
- protein
- Length
- 1,325 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin B; 7F
- EC
- 3.4.22.-
- UniProt
- P18177
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toxin B (EC 3.4.22.-) | protein | 543 | 59% helix, 8% strand | P18177 |
| D | 7F | protein | 119 | 8% helix, 50% strand | — |
| C | 7F | protein | 120 | 8% helix, 49% strand | — |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.78 | 0.82 | 84 | empty |
| 2 | 1109 | 0.73 | 0.76 | 80 | empty |
| 3 | 843 | 0.73 | 0.77 | 75 | empty |
| 4 | 160 | 0.50 | 0.78 | 30 | empty |
| 5 | 165 | 0.49 | 0.77 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–C · 962 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 947 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 887 Ų buried · 9 hydrogen bonds · protein-protein
- D–B · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6OQ8 · Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH 7F · 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 P18177
- Elsewhere: RCSB PDB 6OQ8 · PDBe 6OQ8 · UniProt P18177
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