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Crystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine
Analyse Crystal Structure of AlkB in complex with Fe(III) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T4V
- Type
- protein
- Length
- 199 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.732
- Source
- Escherichia coli
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase AlkB
- EC
- 1.14.11.-
- UniProt
- P05050
- Ligands
- MD3, FE
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.732 · 1 distinct chain · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase AlkB (EC 1.14.11.-) | protein | 199 | 15% helix, 35% strand | P05050 |
Ligands and binding sites
- MD3 · N-(carboxycarbonyl)-S-(naphthalen-2-ylmethyl)-L-cysteine · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- GOL · Glycerol · 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 | 274 | 0.72 | 0.86 | 38 | FE, MD3, GOL |
Compared structures
- 3T4V · Crystal structure of alkb in complex with FE(III) and N-oxalyl-S-(2… · 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 0.98
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 3T4V · PDBe 3T4V · UniProt P05050
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