Research workbench
Crystal structure of P[6] rotavirus
Analyse Crystal structure of P[6] rotavirus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NIW
- Type
- protein
- Length
- 633 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease-sensitive outer capsid protein
- UniProt
- D2DXN5
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease-sensitive outer capsid protein | protein | 158 | 10% helix, 58% strand | D2DXN5 |
| B, C | Protease-sensitive outer capsid protein | protein | 159 | 10% helix, 57% strand | D2DXN5 |
| D | Protease-sensitive outer capsid protein | protein | 157 | 8% helix, 56% strand | D2DXN5 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.75 | 0.91 | 43 | PEG |
| 2 | 449 | 0.72 | 0.82 | 65 | PEG |
| 3 | 357 | 0.59 | 0.76 | 45 | empty |
| 4 | 246 | 0.55 | 0.77 | 31 | empty |
| 5 | 65 | 0.34 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 768 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 747 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 268 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6NIW · Crystal structure of P[6] rotavirus · 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 D2DXN5
- Elsewhere: RCSB PDB 6NIW · PDBe 6NIW · UniProt D2DXN5
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