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Crystal structure of the oligomerization domain of VP35 from ebola virus
Analyse Crystal structure of the oligomerization domain of VP35 from ebola virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GBO
- Type
- protein
- Length
- 852 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase cofactor VP35
- UniProt
- Q05127
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 91% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Polymerase cofactor VP35 | protein | 73 | 92% helix, 0% strand | Q05127 |
| C | Polymerase cofactor VP35 | protein | 67 | 91% helix, 0% strand | Q05127 |
| D | Polymerase cofactor VP35 | protein | 69 | 90% helix, 0% strand | Q05127 |
| G, H, K, L | Polymerase cofactor VP35 | protein | 72 | 93% helix, 0% strand | Q05127 |
| I | Polymerase cofactor VP35 | protein | 66 | 91% helix, 0% strand | Q05127 |
| J | Polymerase cofactor VP35 | protein | 70 | 87% helix, 0% strand | Q05127 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.82 | 0.84 | 124 | empty |
| 2 | 138 | 0.45 | 0.77 | 22 | empty |
| 3 | 134 | 0.42 | 0.75 | 24 | empty |
| 4 | 66 | 0.33 | 0.76 | 17 | empty |
| 5 | 64 | 0.30 | 0.75 | 12 | empty |
Interfaces
34 interfaces between chains.
- D–F · 1468 Ų buried · 12 hydrogen bonds · protein-protein
- J–L · 1443 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1399 Ų buried · 10 hydrogen bonds · protein-protein
- H–I · 1391 Ų buried · 10 hydrogen bonds · protein-protein
- G–K · 1128 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6GBO · Crystal Structure of the oligomerization domain of Vp35 from Ebola virus · 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 6GBO · PDBe 6GBO · UniProt Q05127
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