Research workbench
Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH8535
Analyse Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PZ1
- Type
- protein
- Length
- 933 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.45
- Source
- Mus musculus
- Molecule
- N-glycosylase/DNA lyase
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- O08760
- Ligands
- 8HA, NI
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.45 · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | N-glycosylase/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 313 | 47% helix, 12% strand | O08760 |
| BBB | N-glycosylase/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 308 | 49% helix, 13% strand | O08760 |
| CCC | N-glycosylase/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 312 | 50% helix, 11% strand | O08760 |
Ligands and binding sites
- 8HA · 4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(3-methoxy-4-methyl-phenyl)piperidine-1-carboxamide · ligand · chains AAA
- NI · Nickel (II) ion · metal · chains AAA, BBB, CCC
- EDO · 1,2-ethanediol · additive · chains BBB
- GOL · Glycerol · additive · chains CCC
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.72 | 0.80 | 70 | 8HA |
| 2 | 484 | 0.72 | 0.81 | 56 | empty |
| 3 | 471 | 0.67 | 0.78 | 51 | empty |
| 4 | 139 | 0.58 | 0.83 | 24 | empty |
| 5 | 69 | 0.55 | 0.88 | 16 | empty |
Interfaces
3 interfaces between chains.
- AAA–BBB · 362 Ų buried · 7 hydrogen bonds · protein-protein
- BBB–CCC · 246 Ų buried · 6 hydrogen bonds · protein-protein
- AAA–CCC · 231 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- O08760 · AlphaFold monomer V2.0 prediction for N-GLYCOSYLASE/DNA lyase (O08760) · a predicted model of the same protein · chain BBB against A, TM-score 0.99
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 O08760
- Elsewhere: RCSB PDB 7PZ1 · PDBe 7PZ1 · UniProt O08760
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