MolNFT v1 · #122752 · protein
Protruding domain of GII.4 human norovirus CHDC2094 in complex with 3- fucosyllactose (3FL)
5IYW · VP1: “Protruding domain of GII.4 human norovirus CHDC2094 in complex with 3- fucosyllactose (3FL)”. X-ray diffraction, 3 ligands (GLC, FUC, GAL), 7 pockets (best druggability 0.69). MolNFT v1 #122752 on GenesisL1: 3D structure…
- PDB
- 5IYW
- Type
- protein
- Length
- 609 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- D0QJ68
- Ligands
- GLC, FUC, GAL
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 303 | 7% helix, 35% strand | D0QJ68 |
| B | VP1 | protein | 306 | 7% helix, 35% strand | D0QJ68 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- FLC · Citrate anion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.69 | 0.98 | 22 | empty |
| 2 | 174 | 0.68 | 0.87 | 34 | empty |
| 3 | 266 | 0.63 | 0.81 | 33 | empty |
| 4 | 246 | 0.62 | 0.81 | 28 | empty |
| 5 | 177 | 0.55 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1900 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5IYW · Protruding domain of GII.4 human norovirus CHDC2094 in complex with 3-fucosyllactose (3FL) · 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 D0QJ68
- Elsewhere: RCSB PDB 5IYW · PDBe 5IYW · UniProt D0QJ68
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