Research workbench
Cryo-EM structure of Murine Norovirus capsid
Analyse Cryo-EM structure of Murine Norovirus capsid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IUK
- Type
- protein
- Length
- 1,531 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Murine norovirus GV/NIH-2410/2005/USA
- Molecule
- Major capsid protein VP1
- UniProt
- B7XA03
- Pockets
- 17 · best druggability 0.76
Structure
electron microscopy · resolution 3.5 · 3 distinct chains · 4% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein VP1 | protein | 513 | 5% helix, 27% strand | B7XA03 |
| B | Major capsid protein VP1 | protein | 516 | 3% helix, 28% strand | B7XA03 |
| C | Major capsid protein VP1 | protein | 502 | 5% helix, 28% strand | B7XA03 |
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.76 | 0.79 | 85 | empty |
| 2 | 414 | 0.76 | 0.85 | 64 | empty |
| 3 | 91 | 0.76 | 0.97 | 20 | empty |
| 4 | 263 | 0.72 | 0.87 | 33 | empty |
| 5 | 350 | 0.60 | 0.77 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3105 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 1945 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1303 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6IUK · Cryo-EM structure of murine norovirus capsid · 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 B7XA03
- Elsewhere: RCSB PDB 6IUK · PDBe 6IUK · UniProt B7XA03
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