Structure of PDB 3khc Chain B Binding Site BS03

Receptor Information
>3khc Chain B (length=207) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EPWQEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMS
VAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAG
YPDFQPDACLINRYAPGAKLSLHQDKAEPDLRAPIVSVSLGLPAIFQFGG
LKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLT
FRQAGKK
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 chain3khc Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3khc Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		N120 Y122 L128 H131 H187 I189 R204 N206 T208 R210
Binding residue
(residue number reindexed from 1)		N112 Y114 L120 H123 H179 I181 R196 N198 T200 R202
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3khc, PDBe:3khc, PDBj:3khc
PDBsum3khc
PubMed20084272
UniProtP05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)

[Back to BioLiP]