Research workbench
Structure of VGRG1 in the type VI secretion VGRG1-TSE6-ef-tu complex embedded in lipid nanodiscs
Analyse Structure of VGRG1 in the type VI secretion VGRG1-TSE6-ef-tu complex embedded… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H3N
- Type
- protein
- Length
- 1,881 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VGRG1
- UniProt
- Q9I741
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | VGRG1 | protein | 627 | 11% helix, 44% strand | Q9I741 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.86 | 0.95 | 42 | empty |
| 2 | 210 | 0.82 | 0.95 | 34 | empty |
| 3 | 917 | 0.81 | 0.83 | 74 | empty |
| 4 | 374 | 0.78 | 0.87 | 32 | empty |
| 5 | 341 | 0.78 | 0.88 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 8464 Ų buried · 192 hydrogen bonds · protein-protein
- A–B · 8463 Ų buried · 203 hydrogen bonds · protein-protein
- B–C · 8369 Ų buried · 197 hydrogen bonds · protein-protein
Compared structures
- 6H3N · Structure of VgrG1 in the Type VI secretion VgrG1-Tse6-EF-Tu complex embedded in lipid… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I741 · AlphaFold monomer V2.0 prediction for type VI secretion system spike protein VGRG1A… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9I741
- Elsewhere: RCSB PDB 6H3N · PDBe 6H3N · UniProt Q9I741
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