Structure of PDB 3t4v Chain A

Receptor sequence

>3t4vA (length=199) Species: 83333 (Escherichia coli K-12)

LAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNC
GHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQP
DACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDP
LKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAG

3D structure

• PDB: 3t4v Dynamic combinatorial mass spectrometry leads to inhibitors of a 2-oxoglutarate-dependent nucleic Acid demethylase.
• Chain: A
• Resolution: 1.732 Å

Enzymatic activity

• Enzyme Commision number: 1.14.11.33: DNA oxidative demethylase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	FE	A	H131 D133 H187	H117 D119 H173
BS02	MD3	A	N120 Y122 L128 H131 D133 I143 S145 F154 W178 R183 H187 I189 R204 N206 T208 R210	N106 Y108 L114 H117 D119 I129 S131 F140 W164 R169 H173 I175 R190 N192 T194 R196	MOAD: ic50=0.5uM PDBbind-CN: -logKd/Ki=6.30,IC50=0.5uM

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:3t4v, PDBe:3t4v, PDBj:3t4v
• PDBsum: 3t4v
• PubMed: 22263962
• UniProt: P05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)