MolNFT v1 · #119411 · protein
Toscana virus nucleocapsid protein
5FVA · Nucleoprotein: “Toscana virus nucleocapsid protein”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.83). MolNFT v1 #119411 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FVA
- Type
- protein
- Length
- 1,452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- P21701
- Ligands
- NA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Nucleoprotein | protein | 248 | 61% helix, 1% strand | P21701 |
| B | Nucleoprotein | protein | 240 | 62% helix, 1% strand | P21701 |
| D | Nucleoprotein | protein | 241 | 63% helix, 0% strand | P21701 |
| E | Nucleoprotein | protein | 227 | 60% helix, 0% strand | P21701 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.83 | 0.85 | 119 | empty |
| 2 | 604 | 0.80 | 0.85 | 79 | empty |
| 3 | 506 | 0.78 | 0.85 | 68 | empty |
| 4 | 347 | 0.74 | 0.86 | 56 | empty |
| 5 | 283 | 0.74 | 0.87 | 39 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1107 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 571 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 360 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 288 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 187 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5FVA · Toscana Virus Nucleocapsid Protein · 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 P21701
- Elsewhere: RCSB PDB 5FVA · PDBe 5FVA · UniProt P21701
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