Research workbench
The structure of VGRG1, the needle tip of the bacterial type VI secretion system
Analyse The structure of VGRG1, the needle tip of the bacterial type VI secretion system in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UHV
- Type
- protein
- Length
- 1,289 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VGRG1, valine-glycine repeat protein G1
- UniProt
- Q9I741
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VGRG1, valine-glycine repeat protein G1 | protein | 644 | 7% helix, 20% strand | Q9I741 |
| B | VGRG1, valine-glycine repeat protein G1 | protein | 645 | 9% helix, 25% strand | Q9I741 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.77 | 0.81 | 67 | NA |
| 2 | 548 | 0.75 | 0.82 | 60 | CL |
| 3 | 597 | 0.72 | 0.80 | 47 | CL |
| 4 | 62 | 0.71 | 0.97 | 21 | empty |
| 5 | 51 | 0.71 | 0.97 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 104 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4UHV · The structure of VgrG1, the needle tip of the bacterial Type VI Secretion System · 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 B against A, TM-score 0.94
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 4UHV · PDBe 4UHV · UniProt Q9I741
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