Research workbench
Atomic model of the VIPA/VIPB/HCP, the type six secretion system non- contractile sheath-tube of vibrio cholerae from cryo-EM
Analyse Atomic model of the VIPA/VIPB/HCP, the type six secretion system non… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MXN
- Type
- protein
- Length
- 4,806 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haemolysin co-regulated protein; Type VI secretion protein
- UniProt
- P72350, A0A085SGI6, A0A085SRC0
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 31% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, 3, 4, 5, 6 | Haemolysin co-regulated protein | protein | 170 | 9% helix, 38% strand | P72350 |
| A, B, C, D, E, F | Type VI secretion protein | protein | 473 | 38% helix, 11% strand | A0A085SGI6 |
| a, b, c, d, e, f | Type VI secretion protein | protein | 158 | 32% helix, 10% strand | A0A085SRC0 |
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 | 1197 | 0.76 | 0.79 | 114 | empty |
| 2 | 751 | 0.75 | 0.79 | 57 | empty |
| 3 | 784 | 0.74 | 0.79 | 57 | empty |
| 4 | 765 | 0.74 | 0.79 | 56 | empty |
| 5 | 725 | 0.74 | 0.79 | 53 | empty |
Interfaces
30 interfaces between chains.
- F–f · 3949 Ų buried · 36 hydrogen bonds · protein-protein
- B–b · 3949 Ų buried · 36 hydrogen bonds · protein-protein
- C–c · 3944 Ų buried · 36 hydrogen bonds · protein-protein
- A–a · 3941 Ų buried · 36 hydrogen bonds · protein-protein
- E–e · 3935 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 5MXN · Atomic model of the VipA/VipB/Hcp, the type six secretion system non-contractile… · the same entry in another collection · chain 1 against 1, 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 P72350
- Every structure of UniProt A0A085SGI6
- Every structure of UniProt A0A085SRC0
- Elsewhere: RCSB PDB 5MXN · PDBe 5MXN · UniProt P72350 · UniProt A0A085SGI6 · UniProt A0A085SRC0
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