7EZQ | pdb_00007ezq

Complex structure of AtHPPD with inhibitor Y15832

• PDB DOI: https://doi.org/10.2210/pdb7EZQ/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-01 Released: 2022-06-01 
• Deposition Author(s): Lin, H.Y., Yang, G.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Complex structure of AtHPPD with inhibitor Y18093

Lin, H.Y., Yang, G.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.7 kDa 
• Atom Count: 3,157 
• Modeled Residue Count: 382 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A	410	Arabidopsis thaliana	Mutation(s): 0  Gene Names: HPD, PDS1, At1g06570, F12K11.9 EC: 1.13.11.27
UniProt
Find proteins for P93836 (Arabidopsis thaliana) Explore P93836  Go to UniProtKB:  P93836

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0O0 (Subject of Investigation/LOI)	B [auth A]	6-(1,3-dimethyl-5-oxidanyl-pyrazol-4-yl)carbonyl-1,5-dimethyl-3-(2-methylphenyl)quinazoline-2,4-dione C23 H22 N4 O4 YKHYFGVAUPZAFT-UHFFFAOYSA-N
CO (Subject of Investigation/LOI)	C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.567	α = 90
b = 83.747	β = 100.25
c = 61.636	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Lin, H.Y., Yang, G.F.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary