Research workbench
Stalk complex structure (TrwJ/VirB5-TrwI/VirB6) from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Analyse Stalk complex structure (TrwJ/VirB5-TrwI/VirB6) from the fully-assembled R388… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O3V
- Type
- protein
- Length
- 2,153 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Escherichia coli
- Molecule
- TrwJ protein; TrwI protein
- UniProt
- O50331, O50333
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.7 · 6 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | TrwJ protein | protein | 198 | 72% helix, 1% strand | O50331 |
| F | TrwI protein | protein | 261 | 89% helix, 0% strand | O50333 |
| G | TrwI protein | protein | 261 | 87% helix, 0% strand | O50333 |
| H | TrwI protein | protein | 188 | 87% helix, 1% strand | O50333 |
| I | TrwI protein | protein | 193 | 87% helix, 1% strand | O50333 |
| J | TrwI protein | protein | 260 | 85% helix, 0% strand | O50333 |
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 | 414 | 0.86 | 0.94 | 39 | empty |
| 2 | 365 | 0.84 | 0.93 | 35 | empty |
| 3 | 498 | 0.80 | 0.87 | 35 | empty |
| 4 | 92 | 0.77 | 0.98 | 17 | empty |
| 5 | 661 | 0.75 | 0.81 | 75 | empty |
Interfaces
26 interfaces between chains.
- A–B · 3963 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 3947 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 3945 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 3882 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 3854 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7O3V · Stalk complex structure (TRWJ/VIRB5-TRWI/VIRB6) from the fully- assembled R388 type IV… · 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 O50331
- Every structure of UniProt O50333
- Elsewhere: RCSB PDB 7O3V · PDBe 7O3V · UniProt O50331 · UniProt O50333
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