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Crystal structure of P domain from norovirus strain SAGA4 in complex with hbga type lea (triglycan)
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
- 4WZL
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- B5BTR7
- Ligands
- NDG, GAL, FUC
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | VP1 | protein | 308 | 6% helix, 36% strand | B5BTR7 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains B, A
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.66 | 0.79 | 50 | EDO, ACT |
| 2 | 314 | 0.62 | 0.79 | 35 | ACT |
| 3 | 140 | 0.55 | 0.81 | 21 | empty |
| 4 | 66 | 0.36 | 0.77 | 21 | EDO |
| 5 | 67 | 0.32 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1785 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4WZL · Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type Lea… · 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 B5BTR7
- Elsewhere: RCSB PDB 4WZL · PDBe 4WZL · UniProt B5BTR7
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