Structure of PDB 6ie2 Chain A Binding Site BS02

Receptor Information
>6ie2 Chain A (length=321) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GEDAFRKLFRFYRQSRPGTADLEGVIDFSAGAQKVIKSQLNVSSVSEQNA
YRAGLQPVSKWQAYGLKGYPGFIFIPNPFLPGYQWHWVKQCLKLYSQKPN
VCNLDKHMSKEETQDLWEQSKEFLRYKERSLLEKLRWVTVGYHYNWDSKK
YSADHYTPFPSDLGFLSEQVAAACGFEDFRAEAGILNYYRLDSTLGIHVD
RSELDHSKPLLSFSFGQSAIFLLGGLQRDEAPTAMFMHSGDIMIMSGFSR
LLNHAVPRVLPNPEGEGLPHCLEAPLPAVLPRDSMVEPCSMEDWQVCASY
LKTARVNMTVRQVLATDQNFP
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 chain6ie2 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ie2 Structural basis of nucleic acid recognition and 6mA demethylation by human ALKBH1.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		Y222 L228 H231 D233 H287 V289 R338 N340
Binding residue
(residue number reindexed from 1)		Y189 L195 H198 D200 H254 V256 R305 N307
Annotation score5
Enzymatic activity
Enzyme Commision number 1.14.11.-
1.14.11.33: DNA oxidative demethylase.
1.14.11.51: DNA N(6)-methyladenine demethylase.
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0008198 ferrous iron binding
GO:0016706 2-oxoglutarate-dependent dioxygenase activity
GO:0016829 lyase activity
GO:0035515 oxidative RNA demethylase activity
GO:0035516 broad specificity oxidative DNA demethylase activity
GO:0042056 chemoattractant activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0141131 DNA N6-methyladenine demethylase activity
GO:1990984 tRNA demethylase activity
Biological Process
GO:0001701 in utero embryonic development
GO:0001764 neuron migration
GO:0001890 placenta development
GO:0002101 tRNA wobble cytosine modification
GO:0006281 DNA repair
GO:0006417 regulation of translation
GO:0006446 regulation of translational initiation
GO:0006448 regulation of translational elongation
GO:0010468 regulation of gene expression
GO:0030154 cell differentiation
GO:0031175 neuron projection development
GO:0035513 oxidative RNA demethylation
GO:0042245 RNA repair
GO:0043524 negative regulation of neuron apoptotic process
GO:0048589 developmental growth
GO:0050918 positive chemotaxis
GO:0070129 regulation of mitochondrial translation
GO:0141137 positive regulation of gene expression, epigenetic
GO:1990983 regulation of translational initiation by tRNA modification
Cellular Component
GO:0000791 euchromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6ie2, PDBe:6ie2, PDBj:6ie2
PDBsum6ie2
PubMed32051559
UniProtQ13686|ALKB1_HUMAN Nucleic acid dioxygenase ALKBH1 (Gene Name=ALKBH1)

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