Research workbench
Nodamura virus
Analyse Nodamura virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NOV
- Type
- protein
- Length
- 996 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nodamura virus coat proteins
- UniProt
- P12871
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nodamura virus coat proteins | protein | 309 | 12% helix, 38% strand | P12871 |
| D | Nodamura virus coat proteins | protein | 20 | 75% helix, 0% strand | P12871 |
| E, F | Nodamura virus coat proteins | protein | 17 | 65% helix, 0% strand | P12871 |
| C | Nodamura virus coat proteins | protein | 324 | 17% helix, 37% strand | P12871 |
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.87 | 0.87 | 54 | empty |
| 2 | 286 | 0.75 | 0.87 | 25 | empty |
| 3 | 262 | 0.73 | 0.87 | 29 | empty |
| 4 | 239 | 0.73 | 0.87 | 27 | empty |
| 5 | 172 | 0.55 | 0.80 | 23 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1762 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1761 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1758 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 754 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 697 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1NOV · Nodamura virus · 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 P12871
- Elsewhere: RCSB PDB 1NOV · PDBe 1NOV · UniProt P12871
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