Structure of PDB 3khc Chain B Binding Site BS01

Receptor Information

>3khc Chain B (length=207) Species: 83333 (Escherichia coli K-12)

EPWQEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMS
VAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAG
YPDFQPDACLINRYAPGAKLSLHQDKAEPDLRAPIVSVSLGLPAIFQFGG
LKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLT
FRQAGKK

Ligand information

>3khc Chain C (length=8)

tagtgcct

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3khc Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): T51 G53 Y55 M57 W69 G75 Y76 K127 S129 H131 R161 R210
• Binding residue (residue number reindexed from 1): T43 G45 Y47 M49 W61 G67 Y68 K119 S121 H123 R153 R202
• Binding affinity: PDBbind-CN: Kd=0.316uM

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:3khc, PDBe:3khc, PDBj:3khc
• PDBsum: 3khc
• PubMed: 20084272
• UniProt: P05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)