Research workbench
Crystal structure of TM1821, the 8-oxoguanine DNA glycosylase of thermotoga maritima
Analyse Crystal structure of TM1821, the 8-oxoguanine DNA glycosylase of thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N0U
- Type
- protein
- Length
- 626 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable N-GLYCOSYLASE/DNA lyase
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q9X2E1
- Ligands
- NA
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 209 | 72% helix, 0% strand | Q9X2E1 |
| C | Probable N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 208 | 72% helix, 0% strand | Q9X2E1 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.72 | 0.78 | 72 | NA |
| 2 | 184 | 0.61 | 0.83 | 28 | empty |
| 3 | 189 | 0.61 | 0.82 | 28 | empty |
| 4 | 110 | 0.52 | 0.82 | 25 | empty |
| 5 | 189 | 0.43 | 0.73 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–C · 582 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 335 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3N0U · Crystal structure of Tm1821, the 8-oxoguanine DNA glycosylase of Thermotoga maritima · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X2E1 · AlphaFold monomer V2.0 prediction for 8-oxoguanine DNA GLYCOSYLASE/AP lyase (Q9X2E1) · a predicted model of the same protein · chain C 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 Q9X2E1
- Elsewhere: RCSB PDB 3N0U · PDBe 3N0U · UniProt Q9X2E1
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