MolNFT v1 · #117024 · protein
Structure of minor nucleoprotein V30 from zaire ebolavirus
5DVW · Minor nucleoprotein VP30: “Structure of minor nucleoprotein V30 from zaire ebolavirus”. X-ray diffraction, 5 pockets (best druggability 0.68). MolNFT v1 #117024 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DVW
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Minor nucleoprotein VP30
- UniProt
- Q05323
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Minor nucleoprotein VP30 | protein | 132 | 67% helix, 0% strand | Q05323 |
| B | Minor nucleoprotein VP30 | protein | 130 | 68% helix, 0% strand | Q05323 |
| C, D | Minor nucleoprotein VP30 | protein | 127 | 70% helix, 0% strand | Q05323 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.68 | 0.76 | 86 | empty |
| 2 | 404 | 0.60 | 0.77 | 41 | empty |
| 3 | 73 | 0.33 | 0.74 | 12 | empty |
| 4 | 51 | 0.29 | 0.75 | 13 | empty |
| 5 | 55 | 0.28 | 0.73 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1688 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1614 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 415 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 346 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DVW · Structure of minor nucleoprotein V30 from Zaire ebolavirus · 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 Q05323
- Elsewhere: RCSB PDB 5DVW · PDBe 5DVW · UniProt Q05323
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