MolNFT v1 · #36689 · protein + DNA
Crystal structure of alkb in complex with CO(II), 2-oxoglutarate, and methylated trinucleotide T-mea-T
2FDF · 5'-D(P*TP*(MA7)P*T)-3': “Crystal structure of alkb in complex with CO(II), 2-oxoglutarate, and methylated trinucleotide T-mea-T”. X-ray diffraction, 2 ligands (AKG, CO). MolNFT v1 #36689 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2FDF
- 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, CO
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 34% 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 | 15% helix, 34% strand | P05050 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- B–A · 534 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2FDF · Crystal Structure of AlkB in complex with Co(II), 2-oxoglutarate, and methylated… · 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 2FDF · PDBe 2FDF · UniProt P05050
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