Research workbench
Crystal structure of pab-agog in complex with 8-oxoguanosine
Analyse Crystal structure of pab-agog in complex with 8-oxoguanosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OLI
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-GLYCOSYLASE/DNA lyase
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q9UZY0
- Ligands
- 8HG
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 242 | 70% helix, 0% strand | Q9UZY0 |
Ligands and binding sites
- 8HG · 2'-deoxy-8-oxoguanosine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.60 | 0.83 | 21 | 8HG |
| 2 | 393 | 0.58 | 0.75 | 29 | empty |
| 3 | 147 | 0.54 | 0.81 | 20 | 8HG, EDO |
Interfaces
1 interface between chains.
- A–B · 352 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 Q9UZY0
- Elsewhere: RCSB PDB 7OLI · PDBe 7OLI · UniProt Q9UZY0
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