MolNFT v1 · #36692 · protein + DNA
Crystal structure of alkb in complex with FE(II), 2-oxoglutarate, and methylated trinucleotide T-mea-T (air 3 hours)
2FDI · 5'-D(P*TP*(MA7)P*T)-3': “Crystal structure of alkb in complex with FE(II), 2-oxoglutarate, and methylated trinucleotide T-mea-T (air 3…”. X-ray diffraction, 2 ligands (AKG, FE2), 1 pocket (best druggability 0.78). MolNFT v1 #36692…
- PDB
- 2FDI
- 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, FE2
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 17% 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 | 17% helix, 35% strand | P05050 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains B, A
- FE2 · Fe (II) ion · metal · chains B, A
- SIN · Succinic acid · additive · chains A
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 | 97 | 0.78 | 0.98 | 26 | FE2, AKG, SIN |
Interfaces
1 interface between chains.
- B–A · 533 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2FDI · Crystal Structure of AlkB in complex with Fe(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 0.99
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 2FDI · PDBe 2FDI · UniProt P05050
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