MolNFT v1 · #69143 · protein
Crystal structure of escherichia COLI alkb with CO(II) and 2-og
3KHB · Alpha-ketoglutarate-dependent dioxygenase alkb: “Crystal structure of escherichia COLI alkb with CO(II) and 2-og”. X-ray diffraction, 2 ligands (AKG, CO), 2 pockets (best druggability 0.65). MolNFT v1 #69143 on GenesisL1: 3D…
- PDB
- 3KHB
- Type
- protein
- Length
- 409 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase alkb
- EC
- 1.14.11.-
- UniProt
- P05050
- Ligands
- AKG, CO
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb (EC 1.14.11.-) | protein | 203 | 14% helix, 34% strand | P05050 |
| B | Alpha-ketoglutarate-dependent dioxygenase alkb (EC 1.14.11.-) | protein | 206 | 17% helix, 39% strand | P05050 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.65 | 0.84 | 33 | CO, AKG |
| 2 | 255 | 0.63 | 0.81 | 40 | CO, AKG |
Compared structures
- 3KHB · Crystal structure of Escherichia coli AlkB with Co(II) and 2-OG · 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 B 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 3KHB · PDBe 3KHB · UniProt P05050
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