Research workbench
Vipa-N2/VIPB contracted sheath of type VI secretion system
Analyse Vipa-N2/VIPB contracted sheath of 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
- 5MYU
- Type
- protein
- Length
- 3,342 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; Type VI secretion system protein impc
- UniProt
- A0A023PRF3, A0A023PTI7
- Pockets
- 20 · best druggability 0.58
Structure
electron microscopy · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, b, c, d, e, f | Uncharacterized protein | protein | 127 | 27% helix, 24% strand | A0A023PRF3 |
| A, B, C, D, E, F | Type VI secretion system protein impc | protein | 430 | 42% helix, 17% strand | A0A023PTI7 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.58 | 0.78 | 24 | empty |
| 2 | 256 | 0.56 | 0.78 | 30 | empty |
| 3 | 263 | 0.55 | 0.77 | 32 | empty |
| 4 | 245 | 0.55 | 0.78 | 27 | empty |
| 5 | 276 | 0.55 | 0.76 | 37 | empty |
Interfaces
12 interfaces between chains.
- d–D · 3704 Ų buried · 38 hydrogen bonds · protein-protein
- b–B · 3697 Ų buried · 38 hydrogen bonds · protein-protein
- f–F · 3688 Ų buried · 38 hydrogen bonds · protein-protein
- a–A · 3683 Ų buried · 38 hydrogen bonds · protein-protein
- e–E · 3677 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5MYU · VipA-N2/VipB contracted sheath of type VI secretion system · the same entry in another collection · chain a against a, TM-score 1.00
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 A0A023PRF3
- Every structure of UniProt A0A023PTI7
- Elsewhere: RCSB PDB 5MYU · PDBe 5MYU · UniProt A0A023PRF3 · UniProt A0A023PTI7
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