Structure of PDB 4nid Chain A Binding Site BS04

Receptor Information
>4nid Chain A (length=203) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAM
TNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPD
FQPDACLINRYAPGAKLCLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKR
NDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQ
AGK
Ligand information
Ligand IDAKG
InChIInChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
InChIKeyKPGXRSRHYNQIFN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(=O)CCC(=O)O
OpenEye OEToolkits 1.7.6C(CC(=O)O)C(=O)C(=O)O
CACTVS 3.385OC(=O)CCC(=O)C(O)=O
FormulaC5 H6 O5
Name2-OXOGLUTARIC ACID
ChEMBLCHEMBL1686
DrugBankDB08845
ZINCZINC000001532519
PDB chain4nid Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4nid Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues.
Resolution1.58 Å
Binding residue
(original residue number in PDB)		N120 Y122 L128 H131 H187 I189 R204 N206
Binding residue
(residue number reindexed from 1)		N109 Y111 L117 H120 H176 I178 R193 N195
Annotation score5
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4nid, PDBe:4nid, PDBj:4nid
PDBsum4nid
PubMed24596302
UniProtP05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)

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