Structure of PDB 5ywk Chain B

Receptor sequence

>5ywkB (length=368) Species: 3702 (Arabidopsis thaliana)

FSKFVRKNPKSDKFKVKRFHHIEFWCGDATNVARRFSWGLGMRFSAKSDL
STGNMVHASYLLTSGDLRFLFTAPYSPSLTTASIPSFDHGSCRSFFSSHG
LGVRAVAIEVEDAESAFSISVANGAIPSSPPIVLNEAVTIAEVKLYGDVV
LRYVSYKAFLPGFERVEDASPLDYGIRRLDHAVGNVPELGPALTYVAGFT
GFHQFAEFSGLNSAVLASNDEMVLLPINEPVKSQIQTYLEHNEGAGLQHL
ALMSEDIFRTLREMRKRSSIGGFDFMPSPPPTYYQNLKKRVGDVLSDDQI
KECEELGILVDRDDQGTLLQIFTKPLGDRPTIFIEIIQRVGCMMYQSGGC
GGFGKGNFSELFKSIEEY

3D structure

• PDB: 5ywk Structure-Guided Discovery of Silicon-Containing Subnanomolar Inhibitor of Hydroxyphenylpyruvate Dioxygenase as a Potential Herbicide.
• Chain: B
• Resolution: 2.804 Å

Enzymatic activity

• Enzyme Commision number: 1.13.11.27: 4-hydroxyphenylpyruvate dioxygenase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	CO	B	H226 H308 E394	H181 H249 E335
BS02	92X	B	H226 S267 P280 N282 H308 F381 E394 F419 G420 F424	H181 S213 P226 N228 H249 F322 E335 F353 G354 F358

Gene Ontology

Molecular Function

• GO:0003868 4-hydroxyphenylpyruvate dioxygenase activity
• GO:0005506 iron ion binding
• GO:0016701 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

Biological Process

• GO:0006559 L-phenylalanine catabolic process
• GO:0006572 tyrosine catabolic process
• GO:0009072 aromatic amino acid metabolic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5ywk, PDBe:5ywk, PDBj:5ywk
• PDBsum: 5ywk
• PubMed: 33395281
• UniProt: P93836|HPPD_ARATH 4-hydroxyphenylpyruvate dioxygenase (Gene Name=HPD)