Research workbench
CDTb Double Heptamer Short Form Modeled from Cryo-EM Map Reconstructed using C7 Symmetry
Analyse CDTb Double Heptamer Short Form Modeled from Cryo-EM Map Reconstructed using C7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O2N
- Type
- protein
- Length
- 9,218 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Clostridioides difficile
- Molecule
- ADP-ribosyltransferase binding component
- UniProt
- A8DS70
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.7 · 3 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, H, J, L | ADP-ribosyltransferase binding component | protein | 659 | 10% helix, 39% strand | A8DS70 |
| C, E, G, I, K, M | ADP-ribosyltransferase binding component | protein | 658 | 9% helix, 29% strand | A8DS70 |
| Z | ADP-ribosyltransferase binding component | protein | 657 | 8% helix, 30% strand | A8DS70 |
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 | 865 | 0.84 | 0.86 | 96 | empty |
| 2 | 811 | 0.84 | 0.87 | 90 | empty |
| 3 | 1031 | 0.84 | 0.85 | 113 | empty |
| 4 | 782 | 0.83 | 0.86 | 83 | empty |
| 5 | 777 | 0.83 | 0.86 | 80 | empty |
Interfaces
35 interfaces between chains.
- J–L · 4143 Ų buried · 50 hydrogen bonds · protein-protein
- B–D · 4139 Ų buried · 46 hydrogen bonds · protein-protein
- F–H · 4131 Ų buried · 59 hydrogen bonds · protein-protein
- D–F · 4120 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 4118 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 6O2N · Cdtb double heptamer short form modeled from cryo-EM MAP reconstructed using C7 symmetry · 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 A8DS70
- Elsewhere: RCSB PDB 6O2N · PDBe 6O2N · UniProt A8DS70
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