Research workbench
Crystal structure of P domain from norwalk virus strain vietnam 026 in complex with fucose
Analyse Crystal structure of P domain from norwalk virus strain vietnam 026 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ONY
- Type
- protein
- Length
- 928 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q5F4T5
- Ligands
- FUC
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 310 | 8% helix, 37% strand | Q5F4T5 |
| B, C | Capsid protein | protein | 309 | 8% helix, 38% strand | Q5F4T5 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.79 | 0.80 | 126 | EDO |
| 2 | 209 | 0.63 | 0.83 | 30 | EDO |
| 3 | 128 | 0.42 | 0.76 | 24 | empty |
| 4 | 109 | 0.39 | 0.75 | 24 | empty |
| 5 | 61 | 0.31 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1929 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 305 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3ONY · Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with Fucose · 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 Q5F4T5
- Elsewhere: RCSB PDB 3ONY · PDBe 3ONY · UniProt Q5F4T5
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