8QNK | pdb_00008qnk

OPR3 variant R283D in complex with NADPH4

PDB DOI: https://doi.org/10.2210/pdb8QNK/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.222 (Depositor), 0.224 (DCC)
R-Value Work:
0.195 (Depositor), 0.199 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 180.87 kDa
Atom Count: 12,395
Modelled Residue Count: 1,466
Deposited Residue Count: 1,608
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12-oxophytodienoate reductase 3	A, B, C, D	402	Solanum lycopersicum	Mutation(s): 1 Gene Names: OPR3 EC: 1.3.1.42
UniProt
Find proteins for Q9FEW9 (Solanum lycopersicum) Explore Q9FEW9 Go to UniProtKB: Q9FEW9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9FEW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5J8 (Subject of Investigation/LOI) Query on 5J8 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C]	F [auth A], J [auth C]	[[(2R,3S,4R,5R)-5-(5-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate C₂₁ H₃₂ N₇ O₁₇ P₃ XBYZUJOLVDCGQT-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth C]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth C], K [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]