Research workbench
Iron-catalyzed oxidation intermediates captured in a DNA repair dioxygenase
Analyse Iron-catalyzed oxidation intermediates captured in a DNA repair dioxygenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O1M
- Type
- protein + DNA
- Length
- 226 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase alkb; DNA…
- EC
- 1.14.11.-
- UniProt
- P05050
- Ligands
- AKG, MN
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb (EC 1.14.11.-) | protein | 201 | 15% helix, 35% strand | P05050 |
| B | DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(ME6)P*AP*CP*CP*GP*T)-3') | dna | 12 | — | — |
| C | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3') | dna | 13 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.58 | 0.82 | 21 | empty |
| 2 | 294 | 0.55 | 0.76 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 711 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 638 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- A–C · 223 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3O1M · Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase · the same entry in another collection · chain C against C, TM-score 1.00
- P05050 · AlphaFold monomer V2.0 prediction for alpha-ketoglutarate-dependent dioxygenase alkb… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P05050
- Elsewhere: RCSB PDB 3O1M · PDBe 3O1M · UniProt P05050
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