Research workbench
Crystal structure of alkb protein with cofactors bound to dsdna containing M6A
Analyse Crystal structure of alkb protein with cofactors bound to dsdna containing M6A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NID
- Type
- protein + DNA
- Length
- 228 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
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb (EC 1.14.11.33) | protein | 203 | 15% helix, 36% 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
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 | 252 | 0.57 | 0.79 | 29 | empty |
| 2 | 165 | 0.57 | 0.82 | 20 | empty |
| 3 | 108 | 0.33 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 774 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 635 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–C · 220 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4NID · Crystal structure of AlkB protein with cofactors bound to dsDNA containing m6A · 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 4NID · PDBe 4NID · UniProt P05050
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