Structure of PDB 6ypv Chain A Binding Site BS01

Receptor Information

>6ypv Chain A (length=199) Species: 83333 (Escherichia coli K-12)

LAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNC
GHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQP
DACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDP
LKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAG

Ligand information

• Ligand ID: FE
• InChI: InChI=1S/Fe/q+3
• InChIKey: VTLYFUHAOXGGBS-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  CACTVS 3.341
  OpenEye OEToolkits 1.5.0: [Fe+3]
• Formula: Fe
• Name: FE (III) ION
• DrugBank: DB13949
• PDB chain: 6ypv Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ypv Anaerobic fixed-target serial crystallography.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): H131 D133 H187
• Binding residue (residue number reindexed from 1): H117 D119 H173
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.14.11.33: DNA oxidative demethylase.

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008198 ferrous iron binding
• GO:0035515 oxidative RNA demethylase activity
• GO:0035516 broad specificity oxidative DNA demethylase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

Biological Process

• GO:0006281 DNA repair
• GO:0006307 DNA alkylation repair
• GO:0035513 oxidative RNA demethylation
• GO:0042245 RNA repair
• GO:0070989 oxidative demethylation
• GO:0072702 response to methyl methanesulfonate

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:6ypv, PDBe:6ypv, PDBj:6ypv
• PDBsum: 6ypv
• PubMed: 32939282
• UniProt: P05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)