Research workbench
Crystal structure of tga-agog, an 8-oxoguanine DNA glycosylase from thermococcus gammatolerans
Analyse Crystal structure of tga-agog, an 8-oxoguanine DNA glycosylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OU3
- Type
- protein
- Length
- 489 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
- C5A7E3
- Ligands
- CL
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 72% 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 | 248 | 73% helix, 1% strand | C5A7E3 |
| B | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 241 | 72% helix, 0% strand | C5A7E3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.67 | 0.78 | 37 | empty |
| 2 | 425 | 0.64 | 0.78 | 42 | empty |
| 3 | 265 | 0.60 | 0.80 | 29 | GOL |
| 4 | 98 | 0.39 | 0.76 | 19 | empty |
| 5 | 64 | 0.33 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 447 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7OU3 · Crystal structure of Tga-AGOG, an 8-oxoguanine DNA glycosylase from Thermococcus… · the same entry in another collection · chain A against A, TM-score 1.00
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 C5A7E3
- Elsewhere: RCSB PDB 7OU3 · PDBe 7OU3 · UniProt C5A7E3
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