Research workbench
Crystal structure of PA0091 VGRG1, the central spike of the type VI secretion system
Analyse Crystal structure of PA0091 VGRG1, the central spike of the type VI secretion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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