Research workbench
Crystal structure of catalytically active human 8-oxoguanine glycosylase distally crosslinked to guanine-containing DNA
Analyse Crystal structure of catalytically active human 8-oxoguanine glycosylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IH7
- Type
- protein + DNA
- Length
- 339 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-GLYCOSYLASE/DNA lyase; 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- O15527
- Pockets
- 6 · 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 | 313 | 49% helix, 12% strand | O15527 |
| B | 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' | dna | 14 | — | — |
| C | 5'-D(AP*TP*CP*TP*GP*GP*AP*CP*CP*TP*GP*CP*A)-3' | dna | 12 | — | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.61 | 0.75 | 44 | empty |
| 2 | 54 | 0.52 | 0.88 | 16 | empty |
| 3 | 139 | 0.46 | 0.77 | 24 | empty |
| 4 | 51 | 0.27 | 0.75 | 12 | empty |
| 5 | 60 | 0.27 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 806 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 520 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–B · 442 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3IH7 · Crystal structure of catalytically active human 8-oxoguanine glycosylase distally… · 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 3IH7 · PDBe 3IH7 · UniProt O15527
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