Research workbench
Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction domain, VP5CT
Analyse Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SLQ
- Type
- protein
- Length
- 1,604 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP4
- UniProt
- Q91HI9
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP4 | protein | 270 | 8% helix, 53% strand | Q91HI9 |
| B | VP4 | protein | 269 | 10% helix, 53% strand | Q91HI9 |
| C | VP4 | protein | 266 | 8% helix, 54% strand | Q91HI9 |
| D | VP4 | protein | 267 | 7% helix, 55% strand | Q91HI9 |
| E | VP4 | protein | 267 | 12% helix, 54% strand | Q91HI9 |
| F | VP4 | protein | 265 | 8% helix, 55% strand | Q91HI9 |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.83 | 0.85 | 108 | empty |
| 2 | 761 | 0.82 | 0.85 | 97 | empty |
| 3 | 305 | 0.61 | 0.79 | 43 | empty |
| 4 | 414 | 0.60 | 0.75 | 64 | empty |
| 5 | 430 | 0.60 | 0.75 | 41 | empty |
Interfaces
12 interfaces between chains.
- D–F · 2271 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2202 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 2193 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2185 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2157 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1SLQ · Crystal structure of the trimeric state of the rhesus rotavirus VP4 membrane interaction… · 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 Q91HI9
- Elsewhere: RCSB PDB 1SLQ · PDBe 1SLQ · UniProt Q91HI9
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