MolNFT v2 · #212750 · protein
Crystal structure of P domain from norovirus GI.4 capsid protein in complex with broad specificity antibody single-chain Fv fragment CV-2F5.
8I5L: “Crystal structure of P domain from norovirus GI.4 capsid protein in complex with broad specificity antibody…”. X-ray diffraction at 2.7, 12 pockets (best druggability 0.85). MolNFT v2 #212750 on GenesisL1: 3D structure, binding…
- PDB
- 8I5L
- Type
- protein
- Length
- 1,376 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Chiba virus; Homo sapiens
- Molecule
- Capsid protein; scFv fragment
- UniProt
- Q9DU46
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.7 · 5 distinct chains · 7% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 309 | 7% helix, 30% strand | Q9DU46 |
| B | Capsid protein | protein | 303 | 7% helix, 32% strand | Q9DU46 |
| C | Capsid protein | protein | 305 | 7% helix, 28% strand | Q9DU46 |
| D | scFv fragment | protein | 229 | 5% helix, 50% strand | — |
| E | scFv fragment | protein | 230 | 5% helix, 52% strand | — |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.85 | 0.87 | 110 | empty |
| 2 | 55 | 0.68 | 0.96 | 20 | empty |
| 3 | 709 | 0.67 | 0.75 | 78 | empty |
| 4 | 394 | 0.60 | 0.76 | 31 | empty |
| 5 | 173 | 0.46 | 0.75 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1845 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 739 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 737 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 711 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 269 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 Q9DU46
- Elsewhere: RCSB PDB 8I5L · PDBe 8I5L · UniProt Q9DU46
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