MolNFT v1 · #149923 · protein
X-ray structure of the yersinia pseudotuberculosis ATPase dotb
6GEF · Type IV secretion system protein dotb: “X-ray structure of the yersinia pseudotuberculosis ATPase dotb”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #149923 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6GEF
- Type
- protein
- Length
- 2,313 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV secretion system protein dotb
- UniProt
- A0A0U1QTI9
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type IV secretion system protein dotb | protein | 388 | 38% helix, 26% strand | A0A0U1QTI9 |
| B | Type IV secretion system protein dotb | protein | 384 | 38% helix, 26% strand | A0A0U1QTI9 |
| C | Type IV secretion system protein dotb | protein | 385 | 37% helix, 25% strand | A0A0U1QTI9 |
| D, E | Type IV secretion system protein dotb | protein | 385 | 36% helix, 24% strand | A0A0U1QTI9 |
| F | Type IV secretion system protein dotb | protein | 386 | 36% helix, 27% strand | A0A0U1QTI9 |
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 | 922 | 0.83 | 0.84 | 93 | empty |
| 2 | 766 | 0.81 | 0.84 | 75 | empty |
| 3 | 483 | 0.81 | 0.88 | 54 | empty |
| 4 | 1196 | 0.81 | 0.82 | 113 | empty |
| 5 | 761 | 0.81 | 0.84 | 79 | empty |
Interfaces
7 interfaces between chains.
- E–F · 2021 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1914 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1863 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1814 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 1694 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6GEF · X-ray structure of the Yersinia pseudotuberculosis ATPase DotB · 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 A0A0U1QTI9
- Elsewhere: RCSB PDB 6GEF · PDBe 6GEF · UniProt A0A0U1QTI9
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