Research workbench
Epstein-Barr virus uracil-DNA glycosylase in complex with Ugi from PBS-2
Analyse Epstein-Barr virus uracil-DNA glycosylase in complex with Ugi from PBS-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J8X
- Type
- protein
- Length
- 623 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- BACILLUS PHAGE PBS2; EPSTEIN-BARR VIRUS
- Molecule
- Uracil-DNA glycosylase; Uracil-DNA glycosylase inhibitor
- EC
- 3.2.2.3
- UniProt
- Q777D9, P14739
- Ligands
- URE
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.3 · 4 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uracil-DNA glycosylase (EC 3.2.2.3) | protein | 230 | 38% helix, 11% strand | Q777D9 |
| B | Uracil-DNA glycosylase inhibitor | protein | 83 | 20% helix, 40% strand | P14739 |
| C | Uracil-DNA glycosylase (EC 3.2.2.3) | protein | 229 | 38% helix, 11% strand | Q777D9 |
| D | Uracil-DNA glycosylase inhibitor | protein | 81 | 20% helix, 41% strand | P14739 |
Ligands and binding sites
- URE · Urea · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.72 | 0.78 | 87 | empty |
| 2 | 52 | 0.68 | 0.97 | 22 | empty |
| 3 | 103 | 0.53 | 0.83 | 31 | empty |
| 4 | 80 | 0.51 | 0.84 | 20 | URE |
| 5 | 100 | 0.51 | 0.82 | 22 | URE |
Interfaces
4 interfaces between chains.
- C–D · 1204 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1194 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 734 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 148 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2J8X · Epstein-barr virus uracil-DNA glycosylase in complex with ugi from pbs-2 · 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 Q777D9
- Every structure of UniProt P14739
- Elsewhere: RCSB PDB 2J8X · PDBe 2J8X · UniProt Q777D9 · UniProt P14739
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.