Research workbench
Human 8-oxoguanine glycosylase interrogating fully intrahelical undamaged DNA
Analyse Human 8-oxoguanine glycosylase interrogating fully intrahelical undamaged DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W0R
- Type
- protein + DNA
- Length
- 323 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*AP*GP*GP*TP*C)-3'); DNA (5'-D(P*CP*CP*TP*GP*G)-3')
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- O15527
- Ligands
- S5Y, NA, NO3
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 48% 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 | 312 | 48% helix, 12% strand | O15527 |
| B | DNA (5'-D(P*CP*AP*GP*GP*TP*C)-3') | dna | 6 | — | — |
| C | DNA (5'-D(P*CP*CP*TP*GP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- S5Y · 2-(2-ethoxyethoxy)ethanethiol · ligand · chains A, B, C
- NA · Sodium ion · metal · chains A, B
- NO3 · Nitrate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.68 | 0.80 | 39 | empty |
| 2 | 244 | 0.62 | 0.81 | 39 | NO3 |
| 3 | 189 | 0.51 | 0.78 | 27 | NO3 |
| 4 | 76 | 0.47 | 0.83 | 14 | S5Y |
Interfaces
3 interfaces between chains.
- A–B · 352 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 219 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 217 Ų buried · 14 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6W0R · Human 8-oxoguanine glycosylase interrogating fully intrahelical undamaged 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 0.98
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 O15527
- Elsewhere: RCSB PDB 6W0R · PDBe 6W0R · UniProt O15527
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