Research workbench
Human 8-oxoguanine glycosylase crosslinked with oxog lesion containing DNA
Analyse Human 8-oxoguanine glycosylase crosslinked with oxog lesion containing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W0M
- Type
- protein + DNA
- Length
- 342 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-GLYCOSYLASE/DNA lyase; DNA (5'-D(P*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*C)-3'); DNA…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- O15527
- Ligands
- S5Y, MG
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 314 | 49% helix, 12% strand | O15527 |
| B | DNA (5'-D(P*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*C)-3') | dna | 13 | — | — |
| C | DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)- 3') | dna | 15 | — | — |
Ligands and binding sites
- S5Y · 2-(2-ethoxyethoxy)ethanethiol · ligand · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.61 | 0.75 | 43 | empty |
| 2 | 76 | 0.48 | 0.83 | 18 | empty |
| 3 | 140 | 0.46 | 0.77 | 18 | empty |
| 4 | 125 | 0.40 | 0.75 | 18 | S5Y |
| 5 | 50 | 0.27 | 0.75 | 7 | empty |
Interfaces
3 interfaces between chains.
- A–B · 759 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 556 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–C · 470 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 6W0M · Human 8-oxoguanine glycosylase crosslinked with oxoG lesion containing DNA · the same entry in another collection · chain A against A, 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 6W0M · PDBe 6W0M · UniProt O15527
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