Research workbench
Structure of the mouse 8-oxoguanine DNA glycosylase MOGG1 in complex with ligand TH5675
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
- 6G3Y
- Type
- protein
- Length
- 947 residues
- Chains
- 3
- 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
- O08760
- Ligands
- ELB, NI
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 316 | 48% helix, 11% strand | O08760 |
| C | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 315 | 49% helix, 11% strand | O08760 |
Ligands and binding sites
- ELB · 4-(4-azanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide · ligand · 3 copies · chains A, C, B
- NI · Nickel (II) ion · metal · chains A, B, C
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.77 | 0.83 | 77 | ELB |
| 2 | 582 | 0.73 | 0.81 | 65 | ELB, ACT |
| 3 | 221 | 0.71 | 0.87 | 29 | ELB |
| 4 | 67 | 0.54 | 0.87 | 15 | empty |
| 5 | 51 | 0.53 | 0.89 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 556 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 386 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6G3Y · Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH5675 · the same entry in another collection · chain A against A, TM-score 1.00
- O08760 · AlphaFold monomer V2.0 prediction for N-GLYCOSYLASE/DNA lyase (O08760) · 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 O08760
- Elsewhere: RCSB PDB 6G3Y · PDBe 6G3Y · UniProt O08760
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