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Crystal structure of zaire ebola VP35 interferon inhibitory domain K339A mutant
Analyse Crystal structure of zaire ebola VP35 interferon inhibitory domain K339A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L28
- Type
- protein
- Length
- 728 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase cofactor VP35
- UniProt
- Q05127
- Ligands
- NA, CL, SO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Polymerase cofactor VP35 | protein | 123 | 51% helix, 13% strand | Q05127 |
| E | Polymerase cofactor VP35 | protein | 116 | 46% helix, 15% strand | Q05127 |
| F | Polymerase cofactor VP35 | protein | 120 | 49% helix, 13% strand | Q05127 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains B, C, D, A, E, F
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.78 | 0.90 | 33 | SO4, NA |
| 2 | 369 | 0.74 | 0.85 | 44 | CL, SO4, NA |
| 3 | 399 | 0.66 | 0.80 | 34 | empty |
| 4 | 333 | 0.64 | 0.79 | 30 | empty |
| 5 | 79 | 0.41 | 0.79 | 18 | SO4 |
Interfaces
8 interfaces between chains.
- A–B · 1045 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1007 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 976 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 702 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 435 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3L28 · Crystal structure of Zaire Ebola VP35 interferon inhibitory domain K339A mutant · 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 Q05127
- Elsewhere: RCSB PDB 3L28 · PDBe 3L28 · UniProt Q05127
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