MolNFT v1 · #105999 · protein
Crystal structure of norovirus oif P domain in complex with lewis a trisaccharide
4RM0 · Capsid protein: “Crystal structure of norovirus oif P domain in complex with lewis a trisaccharide”. X-ray diffraction, 4 ligands (GAL, FUC, NAG), 5 pockets (best druggability 0.78). MolNFT v1 #105999 on GenesisL1: 3D structure…
- PDB
- 4RM0
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q6B7R3
- Ligands
- GAL, FUC, NAG, NDG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 307 | 6% helix, 35% strand | Q6B7R3 |
| B | Capsid protein | protein | 306 | 6% helix, 36% strand | Q6B7R3 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains B
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 | 609 | 0.78 | 0.84 | 83 | empty |
| 2 | 212 | 0.75 | 0.90 | 35 | empty |
| 3 | 71 | 0.33 | 0.76 | 17 | empty |
| 4 | 68 | 0.27 | 0.72 | 16 | empty |
| 5 | 60 | 0.25 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1860 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4RM0 · Crystal structure of Norovirus OIF P domain in complex 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 Q6B7R3
- Elsewhere: RCSB PDB 4RM0 · PDBe 4RM0 · UniProt Q6B7R3
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