MolNFT v1 · #142164 · protein
P domain of GII.13 norovirus capsid complexed with lewis a trisaccharide
5ZVC · Major capsid protein VP1: “P domain of GII.13 norovirus capsid complexed with lewis a trisaccharide”. X-ray diffraction, 3 ligands (NAG, GAL, FUC), 8 pockets (best druggability 0.76). MolNFT v1 #142164 on GenesisL1: 3D structure…
- PDB
- 5ZVC
- Type
- protein
- Length
- 619 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- UniProt
- A0A0D6CBA8
- Ligands
- NAG, GAL, FUC
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein VP1 | protein | 308 | 7% helix, 33% strand | A0A0D6CBA8 |
| B | Major capsid protein VP1 | protein | 311 | 7% helix, 33% strand | A0A0D6CBA8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.76 | 0.89 | 37 | empty |
| 2 | 319 | 0.73 | 0.85 | 58 | empty |
| 3 | 276 | 0.60 | 0.79 | 39 | empty |
| 4 | 62 | 0.54 | 0.87 | 18 | empty |
| 5 | 117 | 0.48 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2220 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5ZVC · P domain of GII.13 norovirus capsid complexed with Lewis A trisaccharide · 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 A0A0D6CBA8
- Elsewhere: RCSB PDB 5ZVC · PDBe 5ZVC · UniProt A0A0D6CBA8
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