MolNFT v1 · #109356 · protein
Crystal structure of P domain from norovirus strain NSW0514 in complex with hbga type lex (triglycan)
4X0C · VP1: “Crystal structure of P domain from norovirus strain NSW0514 in complex with hbga type lex (triglycan)”. X-ray diffraction, 3 ligands (NDG, FUC, GAL), 8 pockets (best druggability 0.75). MolNFT v1 #109356 on GenesisL1: 3D…
- PDB
- 4X0C
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- K4LM89
- Ligands
- NDG, FUC, GAL
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 306 | 6% helix, 35% strand | K4LM89 |
| B | VP1 | protein | 307 | 5% helix, 36% strand | K4LM89 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-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 B, A
- FMT · Formic acid · additive · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.75 | 0.94 | 21 | empty |
| 2 | 63 | 0.73 | 0.98 | 21 | empty |
| 3 | 442 | 0.68 | 0.80 | 55 | FMT |
| 4 | 271 | 0.62 | 0.80 | 29 | empty |
| 5 | 241 | 0.58 | 0.79 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1673 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4X0C · Crystal structure of P domain from norovirus strain NSW0514 in complex with HBGA type Lex… · 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 K4LM89
- Elsewhere: RCSB PDB 4X0C · PDBe 4X0C · UniProt K4LM89
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