7CJK

Complex structure of AtHPPD with inhibitor Y18093

• PDB DOI: https://doi.org/10.2210/pdb7CJK/pdb

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


• Deposited: 2020-07-11 Released: 2021-07-14 
• Deposition Author(s): Lin, H.Y., Yang, G.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

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: 49.39 kDa 
• Atom Count: 3,158 
• Modelled Residue Count: 381 
• Deposited Residue Count: 445 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A	445	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
G0X (Subject of Investigation/LOI)	B [auth A]	3-oxidanyl-2-[3,5,6-tris(chloranyl)-4-[(4-chlorophenyl)methylamino]pyridin-2-yl]carbonyl-cyclohex-2-en-1-one C19 H14 Cl4 N2 O3 MQJYIBCWAJRDCH-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: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.242	α = 90
b = 84.046	β = 100.33
c = 62.685	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: 2021-07-14 
Deposition Author(s): Lin, H.Y., Yang, G.F.

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

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary