MolNFT v1 · #100303 · protein
Crystal structure of PA0091 VGRG1, the central spike of the type VI secretion system
4MTK: “Crystal structure of PA0091 VGRG1, the central spike of the type VI secretion system”. X-ray diffraction, 2 ligands (TAM, SO4), 20 pockets (best druggability 0.87). MolNFT v1 #100303 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4MTK
- Type
- protein
- Length
- 3,762 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VGRG1
- UniProt
- Q9I741
- Ligands
- TAM, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | VGRG1 | protein | 627 | 11% helix, 42% strand | Q9I741 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 2 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 256 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 947 | 0.87 | 0.88 | 121 | SO4 |
| 2 | 222 | 0.82 | 0.95 | 29 | TAM |
| 3 | 216 | 0.82 | 0.95 | 27 | TAM |
| 4 | 167 | 0.81 | 0.97 | 26 | SO4 |
| 5 | 127 | 0.81 | 0.97 | 24 | empty |
Interfaces
9 interfaces between chains.
- A–C · 8651 Ų buried · 205 hydrogen bonds · protein-protein
- B–C · 8609 Ų buried · 211 hydrogen bonds · protein-protein
- A–B · 8595 Ų buried · 214 hydrogen bonds · protein-protein
- E–F · 8567 Ų buried · 198 hydrogen bonds · protein-protein
- D–E · 8563 Ų buried · 199 hydrogen bonds · protein-protein
Compared structures
- 4MTK · Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System · the same entry in another collection · chain C against C, 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 4MTK · PDBe 4MTK · UniProt Q9I741
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