Research workbench
Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle
Analyse Structural basis for broad detection of genogroup II noroviruses by a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V7A
- Type
- protein
- Length
- 1,494 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.297
- Source
- Human calicivirus; Mus musculus
- Molecule
- 5B18 heavy chain; 5B18 kappa chain; Capsid
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · resolution 3.297 · 4 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, E | 5B18 heavy chain | protein | 220 | 7% helix, 50% strand | — |
| G, H | 5B18 kappa chain | protein | 215 | 5% helix, 47% strand | — |
| A | Capsid | protein | 315 | 7% helix, 37% strand | — |
| B | Capsid | protein | 309 | 7% helix, 37% strand | — |
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.76 | 0.96 | 31 | empty |
| 2 | 420 | 0.66 | 0.79 | 53 | empty |
| 3 | 436 | 0.66 | 0.79 | 55 | empty |
| 4 | 390 | 0.56 | 0.74 | 58 | empty |
| 5 | 380 | 0.55 | 0.74 | 57 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2005 Ų buried · 30 hydrogen bonds · protein-protein
- F–G · 1995 Ų buried · 17 hydrogen bonds · protein-protein
- E–H · 1988 Ų buried · 16 hydrogen bonds · protein-protein
- F–B · 476 Ų buried · 1 hydrogen bond · protein-protein
- E–A · 456 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3V7A · Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody… · 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
- Elsewhere: RCSB PDB 3V7A · PDBe 3V7A
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