Research workbench
X-ray structure of the legionella pneumophila ATPase dotb
Analyse X-ray structure of the legionella pneumophila ATPase dotb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GEB
- Type
- protein
- Length
- 4,420 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dotb
- UniProt
- O52185
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Dotb | protein | 369 | 39% helix, 26% strand | O52185 |
| B, H | Dotb | protein | 371 | 40% helix, 25% strand | O52185 |
| C, I | Dotb | protein | 369 | 39% helix, 27% strand | O52185 |
| D, J | Dotb | protein | 368 | 40% helix, 25% strand | O52185 |
| E, K | Dotb | protein | 367 | 38% helix, 26% strand | O52185 |
| F, L | Dotb | protein | 366 | 40% helix, 25% strand | O52185 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 929 | 0.84 | 0.85 | 109 | PO4 |
| 2 | 996 | 0.83 | 0.84 | 118 | empty |
| 3 | 957 | 0.82 | 0.84 | 109 | PO4 |
| 4 | 810 | 0.81 | 0.84 | 86 | PO4 |
| 5 | 788 | 0.81 | 0.84 | 77 | PO4 |
Interfaces
19 interfaces between chains.
- J–K · 1899 Ų buried · 31 hydrogen bonds · protein-protein
- K–L · 1848 Ų buried · 30 hydrogen bonds · protein-protein
- A–F · 1839 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 1804 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1791 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6GEB · X-ray structure of the Legionella pneumophila ATPase DotB · the same entry in another collection · chain I against I, 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 O52185
- Elsewhere: RCSB PDB 6GEB · PDBe 6GEB · UniProt O52185
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