MolNFT v1 · #101359 · protein
Molecular mechanism for self-protection against type VI secretion system in vibrio cholerae
4NOO · Vgrg protein: “Molecular mechanism for self-protection against type VI secretion system in vibrio cholerae”. X-ray diffraction, 5 pockets (best druggability 0.71). MolNFT v1 #101359 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4NOO
- Type
- protein
- Length
- 590 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vgrg protein; Putative uncharacterized protein
- UniProt
- Q9KN42, Q9KN41
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Vgrg protein | protein | 200 | 59% helix, 5% strand | Q9KN42 |
| B, D | Putative uncharacterized protein | protein | 95 | 80% helix, 0% strand | Q9KN41 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.71 | 0.83 | 38 | empty |
| 2 | 335 | 0.70 | 0.83 | 37 | empty |
| 3 | 258 | 0.58 | 0.78 | 34 | empty |
| 4 | 72 | 0.34 | 0.76 | 15 | empty |
| 5 | 71 | 0.33 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1353 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1336 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1161 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 264 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 263 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 4NOO · Molecular mechanism for self-protection against type VI secretion system in Vibrio… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KN41 · AlphaFold monomer V2.0 prediction for antitoxin protein TSIV3 (Q9KN41) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9KN42 · AlphaFold monomer V2.0 prediction for type VI secretion system spike protein VGRG3… · a predicted model of the same protein · chain A against A, TM-score 0.91
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 Q9KN42
- Every structure of UniProt Q9KN41
- Elsewhere: RCSB PDB 4NOO · PDBe 4NOO · UniProt Q9KN42 · UniProt Q9KN41
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