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
- 3O1P
- Type
- protein + DNA
- Length
- 227 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
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb (EC 1.14.11.-) | protein | 202 | 14% helix, 35% strand | P05050 |
| B | DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(EDA)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
- AKG · 2-oxoglutaric acid · ligand · chains A, B
- MN · Manganese (II) ion · metal · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.57 | 0.82 | 20 | empty |
| 2 | 161 | 0.51 | 0.79 | 18 | empty |
| 3 | 110 | 0.33 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 747 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 637 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–C · 213 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3O1P · Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase · the same entry in another collection · chain A against A, 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 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 P05050
- Elsewhere: RCSB PDB 3O1P · PDBe 3O1P · UniProt P05050
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