Research workbench
Crystal structure of alkb in complex with MN(II), 2-oxoglutarate, and methylated trinucleotide T-mea-T
Analyse Crystal structure of alkb in complex with MN(II), 2-oxoglutarate, and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FDH
- Type
- protein + DNA
- Length
- 202 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*TP*(MA7)P*T)-3'; Alkylated DNA repair protein alkb
- UniProt
- P05050
- Ligands
- AKG, MN
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(P*TP*(MA7)P*T)-3' | dna | 3 | — | — |
| A | Alkylated DNA repair protein alkb | protein | 199 | 16% helix, 35% strand | P05050 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.77 | 0.99 | 24 | MN, AKG |
Interfaces
1 interface between chains.
- B–A · 523 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2FDH · Crystal Structure of AlkB in complex with Mn(II), 2-oxoglutarate, and methylated… · the same entry in another collection · chain B against B, 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 0.98
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 2FDH · PDBe 2FDH · UniProt P05050
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