7VO8

Structure of AtHPPD complexed with LSY-1

• PDB DOI: https://doi.org/10.2210/pdb7VO8/pdb

• Classification: OXIDOREDUCTASE/INHIBITOR
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-10-12 Released: 2022-09-21 
• Deposition Author(s): Yang, G.-F., Dong, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.185 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Literature

In vivo diagnostics of abiotic plant stress responses via in situ real-time fluorescence imaging

Fu, Y.X., Liu, S.Y., Guo, W.Y., Dong, J., Nan, J.X., Lin, H.Y., Mei, L.C., Yang, W.C., Yang, G.F.

(2022) Plant Physiol 190: 196-201

• DOI: https://doi.org/10.1093/plphys/kiac273

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: 45.29 kDa 
• Atom Count: 3,188 
• Modelled Residue Count: 383 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A	404	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
7RQ	C [auth A]	N-[6-[[9-(dimethylamino)-12H-benzo[a]phenoxazin-5-yl]amino]hexyl]-4-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3-[oxidanyl(oxidanylidene)-$l^4-azanyl]benzamide C38 H39 N5 O7 JKNRGQRJDMEUPO-UHFFFAOYSA-N
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.185 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.978	α = 90
b = 84.192	β = 99.9
c = 62.216	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: 2022-09-21 
Deposition Author(s): Yang, G.-F., Dong, J.

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

Revision History  

• Version 1.0: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description