Structure of PDB 8hb2 Chain C Binding Site BS02

Receptor Information
>8hb2 Chain C (length=254) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HVNYKVFIYDHIRQIAIPTTNLNSQSSLEDIIDESTSCQSVSTDGSIEID
GLTLIHNFLSESEESKILNMIDTVKWAKSKSGRRKQDYGPKVNFKHKKVK
TDTFVGMPEYADMLLNKMSEYDVKKLGNYQPFEMCNLEYEEVKKSAIEMH
QDDMWIWGNRLISINLINGSVMTLSNDNKSFLCYVHMPHRSLLCMADECR
YDWKHGVLAHHIRGRRIALTMREAAKDFAEGGELYEKYGAELIRLGNIRV
PLSK
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 chain8hb2 Chain C Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8hb2 Structural Basis of Nucleic Acid Recognition and 6mA Demethylation by Caenorhabditis elegans NMAD-1A.
Resolution3.06 Å
Binding residue
(original residue number in PDB)		Y173 H184 D186 H239 R250 R256
Binding residue
(residue number reindexed from 1)		Y139 H150 D152 H205 R216 R222
Annotation score5
Enzymatic activity
Enzyme Commision number 1.14.11.51: DNA N(6)-methyladenine demethylase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0032451 demethylase activity
GO:0035516 broad specificity oxidative DNA demethylase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
GO:0141131 DNA N6-methyladenine demethylase activity
Biological Process
GO:0006260 DNA replication
GO:0010032 meiotic chromosome condensation
GO:0060903 positive regulation of meiosis I
GO:0070988 demethylation
GO:1901046 positive regulation of egg-laying behavior
GO:1905516 positive regulation of fertilization
GO:2000781 positive regulation of double-strand break repair
GO:2001252 positive regulation of chromosome organization
Cellular Component
GO:0005634 nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8hb2, PDBe:8hb2, PDBj:8hb2
PDBsum8hb2
PubMed38255759
UniProtQ8MNT9|NMAD1_CAEEL DNA N6-methyl adenine demethylase (Gene Name=nmad-1)

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