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Crystal structure of alkb D135I mutant protein with cofactors bound to dsdna containing M6A/A
Analyse Crystal structure of alkb D135I mutant protein with cofactors bound to dsdna… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NII
- Type
- protein + DNA
- Length
- 225 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase alkb…
- EC
- 1.14.11.33
- UniProt
- P05050
- Ligands
- AKG, MN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb (EC 1.14.11.33) | protein | 200 | 15% helix, 38% strand | P05050 |
| B | 5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3' | dna | 12 | — | — |
| C | 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
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 | 57 | 0.73 | 0.99 | 26 | MN, AKG |
| 2 | 156 | 0.58 | 0.83 | 20 | empty |
| 3 | 213 | 0.55 | 0.79 | 24 | empty |
| 4 | 87 | 0.29 | 0.72 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 776 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 636 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–C · 222 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4NII · Crystal structure of AlkB D135I mutant protein with cofactors bound to dsDNA containing… · 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 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 4NII · PDBe 4NII · UniProt P05050
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