Structure of PDB 6ypv Chain A Binding Site BS02

Receptor Information
>6ypv Chain A (length=199) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNC
GHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQP
DACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDP
LKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAG
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 chain6ypv 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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PDB6ypv Anaerobic fixed-target serial crystallography.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		N120 Y122 L128 H131 D133 H187 I189 R204 N206 R210
Binding residue
(residue number reindexed from 1)		N106 Y108 L114 H117 D119 H173 I175 R190 N192 R196
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:6ypv, PDBe:6ypv, PDBj:6ypv
PDBsum6ypv
PubMed32939282
UniProtP05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)

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