Research workbench
Crystal structure of GII.10 P domain in complex with 19mM fucose
Analyse Crystal structure of GII.10 P domain in complex with 19mM fucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z4V
- Type
- protein
- Length
- 619 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Norovirus GII.10
- Molecule
- Capsid protein
- UniProt
- Q5F4T5
- Ligands
- FUL, NO3
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 7% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 311 | 7% helix, 36% strand | Q5F4T5 |
| B | Capsid protein | protein | 308 | 7% helix, 36% strand | Q5F4T5 |
Ligands and binding sites
- FUL · beta-L-fucopyranose · sugar · chains A, B
- NO3 · Nitrate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.74 | 0.82 | 69 | EDO |
| 2 | 384 | 0.63 | 0.78 | 50 | EDO |
| 3 | 138 | 0.62 | 0.86 | 22 | empty |
| 4 | 148 | 0.51 | 0.79 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1911 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4Z4V · Crystal structure of GII.10 P domain in complex with 19MM fucose · 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 Q5F4T5
- Elsewhere: RCSB PDB 4Z4V · PDBe 4Z4V · UniProt Q5F4T5
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