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Crystal structure of the oligomerization domain of VP35 from ebola virus, mercury derivative
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
- 6GBP
- Type
- protein
- Length
- 849 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase cofactor VP35
- UniProt
- Q05127
- Ligands
- HG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 90% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Polymerase cofactor VP35 | protein | 72 | 93% helix, 0% strand | Q05127 |
| B, E, F, H, K, L | Polymerase cofactor VP35 | protein | 73 | 96% helix, 0% strand | Q05127 |
| C | Polymerase cofactor VP35 | protein | 70 | 90% helix, 0% strand | Q05127 |
| D | Polymerase cofactor VP35 | protein | 68 | 87% helix, 0% strand | Q05127 |
| I | Polymerase cofactor VP35 | protein | 63 | 86% helix, 0% strand | Q05127 |
| J | Polymerase cofactor VP35 | protein | 66 | 88% helix, 0% strand | Q05127 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 11 copies · chains A, D, F, B, C, E, H, K, G, J, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.82 | 0.84 | 107 | HG |
| 2 | 72 | 0.52 | 0.85 | 16 | HG |
| 3 | 143 | 0.51 | 0.80 | 21 | empty |
| 4 | 155 | 0.43 | 0.75 | 25 | empty |
| 5 | 151 | 0.42 | 0.75 | 24 | empty |
Interfaces
33 interfaces between chains.
- B–C · 1389 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1360 Ų buried · 10 hydrogen bonds · protein-protein
- J–L · 1275 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 1162 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 1160 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6GBP · Crystal Structure of the oligomerization domain of VP35 from Ebola virus, mercury… · the same entry in another collection · chain D against D, 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 6GBP · PDBe 6GBP · UniProt Q05127
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