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The crystal structure of the C-terminal domain of Ebola (Tai Forest) nucleoprotein
Analyse The crystal structure of the C-terminal domain of Ebola (Tai Forest)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E2X
- Type
- protein
- Length
- 794 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Tai Forest ebolavirus
- Molecule
- Np
- UniProt
- B8XCN6
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, G, H | Np | protein | 101 | 47% helix, 16% strand | B8XCN6 |
| E, F | Np | protein | 94 | 53% helix, 17% strand | B8XCN6 |
Ligands and binding sites
- 2PE · Nonaethylene glycol · additive · 4 copies · chains B, D, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.67 | 0.79 | 41 | empty |
| 2 | 522 | 0.67 | 0.78 | 38 | empty |
| 3 | 385 | 0.62 | 0.77 | 49 | empty |
| 4 | 414 | 0.61 | 0.76 | 54 | empty |
| 5 | 396 | 0.58 | 0.75 | 33 | empty |
Interfaces
13 interfaces between chains.
- B–D · 499 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 493 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 489 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 488 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 477 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5E2X · The crystal structure of the C-terminal domain of ebola (tai forest) nucleoprotein · 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 B8XCN6
- Elsewhere: RCSB PDB 5E2X · PDBe 5E2X · UniProt B8XCN6
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