Research workbench
Crystal structure of the oligomerization domain of VP35 from reston virus, mercury derivative
Analyse Crystal structure of the oligomerization domain of VP35 from reston virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GBR
- Type
- protein
- Length
- 270 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase cofactor VP35
- UniProt
- Q8JPY0
- Ligands
- MBO
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 93% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase cofactor VP35 | protein | 67 | 96% helix, 0% strand | Q8JPY0 |
| B | Polymerase cofactor VP35 | protein | 66 | 92% helix, 0% strand | Q8JPY0 |
| C | Polymerase cofactor VP35 | protein | 70 | 93% helix, 0% strand | Q8JPY0 |
| D | Polymerase cofactor VP35 | protein | 67 | 93% helix, 0% strand | Q8JPY0 |
Ligands and binding sites
- MBO · Mercuribenzoic acid · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.57 | 0.85 | 13 | empty |
| 2 | 65 | 0.41 | 0.80 | 11 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1647 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1615 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1253 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1203 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 573 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6GBR · Crystal Structure of the oligomerization domain of VP35 from Reston virus, mercury… · 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 Q8JPY0
- Elsewhere: RCSB PDB 6GBR · PDBe 6GBR · UniProt Q8JPY0
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