MolNFT v1 · #184299 · protein
Crystal structure of pab-agog, an 8-oxoguanine DNA glycosylase from pyrococcus abyssi
7OLB · N-GLYCOSYLASE/DNA lyase: “Crystal structure of pab-agog, an 8-oxoguanine DNA glycosylase from pyrococcus abyssi”. X-ray diffraction, 2 ligands (NA, CL), 1 pocket (best druggability 0.56). MolNFT v1 #184299 on GenesisL1: 3D…
- PDB
- 7OLB
- Type
- protein
- Length
- 242 residues
- Chains
- 1
- 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
- NA, CL
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 242 | 69% helix, 0% strand | Q9UZY0 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.56 | 0.82 | 27 | EDO, CIT, NA |
Compared structures
- 7OLB · Crystal structure of Pab-AGOG, an 8-oxoguanine DNA glycosylase from Pyrococcus abyssi · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UZY0 · AlphaFold monomer V2.0 prediction for N-GLYCOSYLASE/DNA lyase (Q9UZY0) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 7OLB · PDBe 7OLB · UniProt Q9UZY0
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