Structure of PDB 7ekd Chain A Binding Site BS01

Receptor Information
>7ekd Chain A (length=343) Species: 39947 (Oryza sativa Japonica Group) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CFDFRAARRVPETHAWPGLDDHPVVDGGGGGGEDAVPVVDVGAGDAAARV
ARAAEQWGAFLLVGHGVPAALLSRVEERVARVFSLPASEKMRAVRGPGEP
CGYGSPPISSFFSKLMWSEGYTFSPSSLRSELRRLWPKSGDDYLLFCDVM
EEFHKEMRRLADELLRLFLRALGLTGEEVAGVEAERRIGERMTATVHLNW
YPRCPEPRRALGLIAHTDSGFFTFVLQSLVPGLQLFRRGPDRWVAVPAVA
GAFVVNVGDLFHILTNGRFHSVYHRAVVNRDRDRVSLGYFLGPPPDAEVA
PLPEAVPAGRSPAYRAVTWPEYMAVRKKAFATGGSALKMVSTD
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 chain7ekd Chain A Residue 405 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7ekd Evolutionary alterations in gene expression and enzymatic activities of gibberellin 3-oxidase 1 in Oryza.
Resolution1.899 Å
Binding residue
(original residue number in PDB)		Y212 L224 H227 L244 H285 R295 S297 F301
Binding residue
(residue number reindexed from 1)		Y201 L213 H216 L233 H274 R284 S286 F290
Annotation score5
Enzymatic activity
Enzyme Commision number 1.14.11.15: gibberellin 3beta-dioxygenase.
Gene Ontology
Molecular Function
GO:0016707 gibberellin 3-beta-dioxygenase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0009416 response to light stimulus
GO:0009685 gibberellin metabolic process
GO:0009686 gibberellin biosynthetic process

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7ekd, PDBe:7ekd, PDBj:7ekd
PDBsum7ekd
PubMed35046494
UniProtQ9FU53|G3OX2_ORYSJ Gibberellin 3-beta-dioxygenase 2 (Gene Name=GA3OX2)

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