› 6m6d

X-ray diffraction
1.84Å resolution

Structure of HPPD complexed with a synthesized inhibitor

Released:
DOI: 10.2210/pdb6m6d/pdb
PDB entry 6m6d coloured by chain, front view.
PDB entry 6m6d coloured by chain, side view.
PDB entry 6m6d coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Structure-Guided Discovery of Silicon-Containing Subnanomolar Inhibitor of Hydroxyphenylpyruvate Dioxygenase as a Potential Herbicide.
Qu RY, Nan JX, Yan YC, Chen Q, Ndikuryayo F, Wei XF, Yang WC, Lin HY, Yang GF
J Agric Food Chem 69 459-473 (2021)
PMID: 33395281

Function and Biology Details

Reaction catalysed: 
4-hydroxyphenylpyruvate + O(2) = homogentisate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161093 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxyphenylpyruvate dioxygenase Chain: A
Molecule details ›
Chain: A
Length: 445 amino acids
Theoretical weight: 48.87 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: P93836 (Residues: 1-445; Coverage: 100%)
Gene names: At1g06570, F12K11.9, HPD, PDS1
Sequence domains: Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily

Ligands and Environments

2 bound ligands:
Ligand CO 1 x CO
Ligand NJX 1 x NJX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2
Unit cell:
a: 76.568Å b: 83.736Å c: 61.96Å
α: 90° β: 100.47° γ: 90°
R-values:
R R work R free
0.185 0.183 0.215
Expression system: Escherichia coli

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