MolNFT v1 · #102571 · protein
Crystal structure of P domain from norovirus strain farmington hills 2004 in complex with hbga type leb (tetraglycan)
4OPS · Major capsid protein: “Crystal structure of P domain from norovirus strain farmington hills 2004 in complex with hbga type leb…”. X-ray diffraction, 3 ligands (FUC, NAG, GAL), 5 pockets (best druggability 0.70). MolNFT v1 #102571 on…
- PDB
- 4OPS
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- R4I4P2
- Ligands
- FUC, NAG, GAL
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Major capsid protein | protein | 306 | 5% helix, 36% strand | R4I4P2 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- GAL · beta-D-galactopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.70 | 0.96 | 20 | empty |
| 2 | 417 | 0.66 | 0.79 | 51 | empty |
| 3 | 448 | 0.65 | 0.78 | 53 | empty |
| 4 | 102 | 0.52 | 0.83 | 22 | empty |
| 5 | 95 | 0.43 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1778 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4OPS · Crystal structure of P domain from norovirus strain Farmington Hills 2004 in complex with… · 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 R4I4P2
- Elsewhere: RCSB PDB 4OPS · PDBe 4OPS · UniProt R4I4P2
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