Research workbench
Crystal structure of an HOGG1-DNA borohydride trapped intermediate complex
Analyse Crystal structure of an HOGG1-DNA borohydride trapped intermediate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HU0
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'; 5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)…
- EC
- 3.2.2.-
- UniProt
- O15527
- Ligands
- OXG, CA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'- D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | dna | 15 | — | — |
| E | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED) P*GP*TP*CP*TP*AP*CP*C)-3' | dna | 15 | — | — |
| A | 8-oxoguanine DNA glycosylase 1 (EC 3.2.2.-) | protein | 314 | 49% helix, 12% strand | O15527 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.75 | 0.99 | 23 | OXG |
| 2 | 332 | 0.55 | 0.75 | 29 | CA |
| 3 | 83 | 0.47 | 0.82 | 17 | empty |
| 4 | 105 | 0.43 | 0.78 | 16 | empty |
| 5 | 68 | 0.36 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- E–A · 635 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–E · 630 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- D–A · 456 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1HU0 · Crystal structure of an HOGG1-DNA borohydride trapped intermediate complex · the same entry in another collection · chain D against D, 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 1HU0 · PDBe 1HU0 · UniProt O15527
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