MolNFT v1 · #75606 · protein
Crystal structure of P domain dimer of norovirus VA207 complexed with 3'-sialyl-lewis X tetrasaccharide
3PVD · Capsid: “Crystal structure of P domain dimer of norovirus VA207 complexed with 3'-sialyl-lewis X tetrasaccharide”. X-ray diffraction, 4 ligands (NDG, GAL, SIA), 6 pockets (best druggability 0.78). MolNFT v1 #75606 on GenesisL1: 3D…
- PDB
- 3PVD
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid
- UniProt
- Q91H09
- Ligands
- NDG, GAL, SIA, FUC
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid | protein | 299 | 5% helix, 38% strand | Q91H09 |
| B | Capsid | protein | 302 | 5% helix, 38% strand | Q91H09 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.78 | 0.80 | 119 | empty |
| 2 | 155 | 0.72 | 0.90 | 24 | empty |
| 3 | 70 | 0.35 | 0.76 | 14 | empty |
| 4 | 52 | 0.33 | 0.78 | 13 | empty |
| 5 | 68 | 0.30 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1698 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3PVD · Crystal structure of P domain dimer of Norovirus VA207 complexed with 3'-sialyl-Lewis x… · 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 Q91H09
- Elsewhere: RCSB PDB 3PVD · PDBe 3PVD · UniProt Q91H09
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