Research workbench
Catalytically inactive human 8-oxoguanine glycosylase crosslinked to oxog containing DNA
Analyse Catalytically inactive human 8-oxoguanine glycosylase crosslinked to oxog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YQR
- Type
- protein + DNA
- Length
- 342 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'…
- EC
- 3.2.2.-
- UniProt
- O15527
- Ligands
- CA
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' | dna | 14 | — | — |
| C | 5'-D(P*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' | dna | 14 | — | — |
| A | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-) | protein | 314 | 49% helix, 12% strand | O15527 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.54 | 0.75 | 30 | CA |
| 2 | 162 | 0.48 | 0.77 | 19 | empty |
| 3 | 83 | 0.45 | 0.81 | 16 | empty |
| 4 | 129 | 0.36 | 0.73 | 22 | empty |
| 5 | 55 | 0.34 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–A · 765 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 598 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- B–A · 440 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1YQR · Catalytically inactive human 8-oxoguanine glycosylase crosslinked to oxoG containing DNA · the same entry in another collection · chain B against B, TM-score 1.00
- O15527 · AlphaFold monomer V2.0 prediction for N-GLYCOSYLASE/DNA lyase (O15527) · a predicted model of the same protein · chain A 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 O15527
- Elsewhere: RCSB PDB 1YQR · PDBe 1YQR · UniProt O15527
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