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Crystal structure of P domain from norovirus strain SAGA4 in complex with hbga type leb (tetraglycan)
Analyse Crystal structure of P domain from norovirus strain SAGA4 in complex with hbga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OPO
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- B5BTT5
- Ligands
- FUC, NAG, GAL
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 309 | 5% helix, 36% strand | B5BTT5 |
| B | VP1 | protein | 307 | 5% helix, 35% strand | B5BTT5 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- ACT · Acetate ion · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.71 | 0.98 | 23 | empty |
| 2 | 231 | 0.60 | 0.80 | 30 | EDO |
| 3 | 274 | 0.58 | 0.78 | 29 | empty |
| 4 | 222 | 0.58 | 0.79 | 27 | empty |
| 5 | 212 | 0.56 | 0.79 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1872 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4OPO · Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type Leb… · 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 B5BTT5
- Elsewhere: RCSB PDB 4OPO · PDBe 4OPO · UniProt B5BTT5
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