8QNX | pdb_00008qnx

OPR3 variant with redesigned loop 6 (8aa) in complex with NADH4

• PDB DOI: https://doi.org/10.2210/pdb8QNX/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Solanum lycopersicum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-09-27 Released: 2025-04-09 
• Deposition Author(s): Bijelic, A., Macheroux, P., Kerschbaumer, B.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of OPR3 wildtype and variants in complex with NAD(P)H

Kerschbaumer, B., Bijelic, A., Macheroux, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.83 kDa 
• Atom Count: 3,389 
• Modelled Residue Count: 364 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12-oxophytodienoate reductase 3	A	396	Solanum lycopersicum	Mutation(s): 4  Gene Names: OPR3 EC: 1.3.1.42
UniProt
Find proteins for Q9FEW9 (Solanum lycopersicum) Explore Q9FEW9  Go to UniProtKB:  Q9FEW9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WI6 (Subject of Investigation/LOI)	C [auth A]	1,4,5,6-Tetrahydronicotinamide adenine dinucleotide C21 H31 N7 O14 P2 GFDCQHGWOHYWLP-XQYAFYQJSA-N
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.01	α = 90
b = 89.62	β = 90
c = 49.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Bijelic, A., Macheroux, P., Kerschbaumer, B.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	--

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release