MolNFT v1 · #111391 · protein
Structure of ebola virus nucleoprotein N-terminal fragment bound to a peptide derived from ebola VP35
4YPI: “Structure of ebola virus nucleoprotein N-terminal fragment bound to a peptide derived from ebola VP35”. X-ray diffraction, 13 pockets (best druggability 0.79). MolNFT v1 #111391 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4YPI
- Type
- protein
- Length
- 1,500 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; Polymerase cofactor VP35
- UniProt
- P18272, Q05127
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Nucleoprotein | protein | 348 | 67% helix, 6% strand | P18272 |
| G, E, F, H | Polymerase cofactor VP35 | protein | 28 | 39% helix, 4% strand | Q05127 |
| A | Nucleoprotein | protein | 346 | 66% helix, 6% strand | P18272 |
| B, D | Nucleoprotein | protein | 347 | 67% helix, 6% strand | P18272 |
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.79 | 0.81 | 116 | empty |
| 2 | 338 | 0.67 | 0.81 | 37 | empty |
| 3 | 60 | 0.53 | 0.87 | 15 | empty |
| 4 | 68 | 0.41 | 0.80 | 20 | empty |
| 5 | 92 | 0.41 | 0.77 | 20 | empty |
Interfaces
17 interfaces between chains.
- B–F · 1365 Ų buried · 17 hydrogen bonds · protein-protein
- C–G · 1344 Ų buried · 19 hydrogen bonds · protein-protein
- D–H · 1331 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1321 Ų buried · 12 hydrogen bonds · protein-protein
- C–A · 797 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4YPI · Structure of Ebola virus nucleoprotein N-terminal fragment bound to a peptide derived… · the same entry in another collection · chain C against C, 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 P18272
- Every structure of UniProt Q05127
- Elsewhere: RCSB PDB 4YPI · PDBe 4YPI · UniProt P18272 · UniProt Q05127
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