Research workbench
Crystal structure of orsay virus-like particle
Analyse Crystal structure of orsay virus-like particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NWV
- Type
- protein
- Length
- 1,046 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- E9KNV5
- Ligands
- CA
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 355 | 11% helix, 40% strand | E9KNV5 |
| C | Capsid protein | protein | 346 | 12% helix, 42% strand | E9KNV5 |
| B | Capsid protein | protein | 345 | 14% helix, 43% strand | E9KNV5 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.74 | 0.78 | 71 | empty |
| 2 | 423 | 0.73 | 0.83 | 48 | empty |
| 3 | 235 | 0.69 | 0.85 | 31 | empty |
| 4 | 411 | 0.68 | 0.80 | 46 | empty |
| 5 | 258 | 0.66 | 0.83 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2023 Ų buried · 30 hydrogen bonds · protein-protein
- C–B · 1601 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1581 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4NWV · Crystal structure of Orsay virus-like particle · 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 E9KNV5
- Elsewhere: RCSB PDB 4NWV · PDBe 4NWV · UniProt E9KNV5
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