Research workbench
Clostridium difficile binary toxin translocase cdtb in asymmetric tetradecamer conformation
Analyse Clostridium difficile binary toxin translocase cdtb in asymmetric tetradecamer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UWR
- 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 0.82
Structure
electron microscopy · 1 distinct chain · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | ADP-ribosyltransferase binding component | protein | 660 | 12% helix, 41% strand | O32739 |
Ligands and binding sites
- CA · Calcium ion · metal · 42 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
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 | 990 | 0.82 | 0.83 | 116 | empty |
| 2 | 1076 | 0.82 | 0.83 | 119 | empty |
| 3 | 1125 | 0.82 | 0.83 | 118 | empty |
| 4 | 1050 | 0.82 | 0.83 | 119 | empty |
| 5 | 1084 | 0.81 | 0.82 | 119 | empty |
Interfaces
35 interfaces between chains.
- A–B · 4186 Ų buried · 77 hydrogen bonds · protein-protein
- A–G · 4184 Ų buried · 79 hydrogen bonds · protein-protein
- B–C · 4178 Ų buried · 79 hydrogen bonds · protein-protein
- F–G · 4177 Ų buried · 79 hydrogen bonds · protein-protein
- E–F · 4173 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- 6UWR · Clostridium difficile binary toxin translocase CDTb in asymmetric tetradecamer… · 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 O32739
- Elsewhere: RCSB PDB 6UWR · PDBe 6UWR · UniProt O32739
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