Research workbench
Mouse norovirus protruding domain complexed with neutralizing Fab fragment from mab A6.2
Analyse Mouse norovirus protruding domain complexed with neutralizing Fab fragment from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L5J
- Type
- protein
- Length
- 1,469 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Anti mouse norovirus mab A6.2 Fab light chain; Anti mouse norovirus mab…
- UniProt
- Q2V8W4
- Pockets
- 19 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 4% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 305 | 4% helix, 22% strand | Q2V8W4 |
| B | Capsid protein | protein | 304 | 4% helix, 24% strand | Q2V8W4 |
| L, X | Anti mouse norovirus mab A6.2 Fab light chain | protein | 210 | 5% helix, 37% strand | — |
| W, Y | Anti mouse norovirus mab A6.2 Fab heavy chain | protein | 220 | 1% helix, 45% strand | — |
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.85 | 0.89 | 78 | empty |
| 2 | 627 | 0.65 | 0.75 | 51 | empty |
| 3 | 68 | 0.58 | 0.89 | 23 | empty |
| 4 | 422 | 0.57 | 0.74 | 71 | empty |
| 5 | 433 | 0.55 | 0.73 | 43 | empty |
Interfaces
8 interfaces between chains.
- L–W · 2006 Ų buried · 14 hydrogen bonds · protein-protein
- X–Y · 1935 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1890 Ų buried · 13 hydrogen bonds · protein-protein
- A–Y · 711 Ų buried · 4 hydrogen bonds · protein-protein
- B–W · 677 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7L5J · Mouse Norovirus Protruding domain complexed with neutralizing Fab fragment from mAb A6.2 · 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 Q2V8W4
- Elsewhere: RCSB PDB 7L5J · PDBe 7L5J · UniProt Q2V8W4
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