Research workbench
Clostridium difficile binary toxin translocase cdtb tetradecamer in symmetric conformation
Analyse Clostridium difficile binary toxin translocase cdtb tetradecamer in symmetric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UWT
- Type
- protein
- Length
- 9,240 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyltransferase binding component
- UniProt
- O32739
- Ligands
- CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 10% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, I, J, K, L, M, N, A, B, C, D, E, F, G | ADP-ribosyltransferase binding component | protein | 660 | 10% helix, 31% strand | O32739 |
Ligands and binding sites
- CA · Calcium ion · metal · 28 copies · chains H, I, J, K, L, M, N, A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.85 | 0.86 | 102 | empty |
| 2 | 997 | 0.84 | 0.85 | 102 | empty |
| 3 | 956 | 0.84 | 0.85 | 106 | empty |
| 4 | 1165 | 0.83 | 0.84 | 126 | empty |
| 5 | 1136 | 0.83 | 0.84 | 124 | empty |
Interfaces
28 interfaces between chains.
- A–G · 2178 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2162 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 2161 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2139 Ų buried · 32 hydrogen bonds · protein-protein
- J–K · 2117 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6UWT · Clostridium difficile binary toxin translocase CDTb tetradecamer in symmetric conformation · the same entry in another collection · chain H against H, 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 O32739
- Elsewhere: RCSB PDB 6UWT · PDBe 6UWT · UniProt O32739
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