Research workbench
Crystal structure of a VirB8-like protein of type IV secretion system from Rickettsia typhi
Analyse Crystal structure of a VirB8-like protein of type IV secretion system from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O3V
- Type
- protein
- Length
- 278 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Rickettsia typhi
- Molecule
- VirB8-like protein of type IV secretion system
- UniProt
- Q68X84
- Ligands
- SRT
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.95 · 2 distinct chains · 35% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VirB8-like protein of type IV secretion system | protein | 138 | 34% helix, 39% strand | Q68X84 |
| B | VirB8-like protein of type IV secretion system | protein | 140 | 35% helix, 37% strand | Q68X84 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.74 | 0.80 | 57 | SRT |
| 2 | 404 | 0.62 | 0.77 | 31 | empty |
| 3 | 75 | 0.45 | 0.81 | 20 | empty |
| 4 | 77 | 0.44 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1054 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4O3V · Crystal structure of a VIRB8-like protein of type IV secretion system from rickettsia… · 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 Q68X84
- Elsewhere: RCSB PDB 4O3V · PDBe 4O3V · UniProt Q68X84
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