Research workbench
Crystal structure of deaminated P domain from norovirus strain Saga GII-4 in complex with Fuc
Analyse Crystal structure of deaminated P domain from norovirus strain Saga GII-4 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H9V
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.52
- Source
- Norovirus Hu/GII-4/Saga4/2006/JP
- Molecule
- VP1
- UniProt
- B5BTR7
- Ligands
- MFU, MG
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.52 · 2 distinct chains · 6% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 309 | 6% helix, 35% strand | B5BTR7 |
| B | VP1 | protein | 303 | 5% helix, 36% strand | B5BTR7 |
Ligands and binding sites
- MFU · methyl alpha-L-fucopyranoside · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.71 | 0.98 | 21 | empty |
| 2 | 478 | 0.69 | 0.80 | 58 | empty |
| 3 | 402 | 0.66 | 0.79 | 40 | empty |
| 4 | 143 | 0.57 | 0.82 | 22 | empty |
| 5 | 117 | 0.46 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1773 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6H9V · Crystal structure of deaminated P domain from norovirus strain saga gii-4 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 B5BTR7
- Elsewhere: RCSB PDB 6H9V · PDBe 6H9V · UniProt B5BTR7
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