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Crystal structure of the VIRB11 ATPase from the brucella suis type IV secretion system in complex with sulphate
Analyse Crystal structure of the VIRB11 ATPase from the brucella suis type IV secretion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GZA
- Type
- protein
- Length
- 982 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV secretion system protein VIRB11
- EC
- 3.6.1.34
- UniProt
- Q8FXK7
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type IV secretion system protein VIRB11 (EC 3.6.1.34) | protein | 324 | 35% helix, 22% strand | Q8FXK7 |
| B | Type IV secretion system protein VIRB11 (EC 3.6.1.34) | protein | 322 | 34% helix, 22% strand | Q8FXK7 |
| C | Type IV secretion system protein VIRB11 (EC 3.6.1.34) | protein | 336 | 37% helix, 21% strand | Q8FXK7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.83 | 0.84 | 118 | SO4 |
| 2 | 933 | 0.77 | 0.80 | 82 | empty |
| 3 | 795 | 0.74 | 0.79 | 96 | SO4 |
| 4 | 130 | 0.44 | 0.76 | 26 | empty |
| 5 | 52 | 0.37 | 0.80 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1985 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1976 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2GZA · Crystal structure of the VirB11 ATPase from the Brucella Suis type IV secretion system in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8FXK7 · AlphaFold monomer V2.0 prediction for type IV secretion system protein VIRB11 (Q8FXK7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8FXK7
- Elsewhere: RCSB PDB 2GZA · PDBe 2GZA · UniProt Q8FXK7
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