4QOJ

CRYSTAL STRUCTURE OF FMN QUINONE REDUCTASE 2 IN COMPLEX WITH RESVERATROL AT 1.85A

PDB DOI: https://doi.org/10.2210/pdb4QOJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-06-20 Released: 2015-08-12
Deposition Author(s): Serriere, J., Boutin, J.A., Isabet, T., Antoine, M., Ferry, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.198
R-Value Work: 0.179
R-Value Observed: 0.180

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF FMN QUINONE REDUCTASE 2 IN COMPLEX WITH RESVERATROL AT 1.85A

Serriere, J., Boutin, J.A., Isabet, T., Antoine, M., Ferry, G.

To be published.

Macromolecule Content

Total Structure Weight: 53.46 kDa
Atom Count: 3,933
Modelled Residue Count: 458
Deposited Residue Count: 462
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosyldihydronicotinamide dehydrogenase [quinone]	A, B	231	Homo sapiens	Mutation(s): 1 Gene Names: NQO2, NMOR2 EC: 1.10.99.2 (PDB Primary Data), 1.10.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P16083 (Homo sapiens) Explore P16083 Go to UniProtKB: P16083
PHAROS: P16083 GTEx: ENSG00000124588
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16083
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
STL Query on STL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	RESVERATROL C₁₄ H₁₂ O₃ LUKBXSAWLPMMSZ-OWOJBTEDSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
STL	BindingDB: 4QOJ	Ki: 88 (nM) from 1 assay(s)
		Kd: 54 (nM) from 1 assay(s)
		IC50: min: 450, max: 6900 (nM) from 7 assay(s)
		-TΔS: 20.93 (kJ/mol) from 1 assay(s)
		ΔG: -4.10e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.198
R-Value Work: 0.179
R-Value Observed: 0.180
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.96	α = 90
b = 83.91	β = 90
c = 106.19	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
MOLREP	phasing
BUSTER	refinement
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-08-12
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4QOJ

CRYSTAL STRUCTURE OF FMN QUINONE REDUCTASE 2 IN COMPLEX WITH RESVERATROL AT 1.85A

CRYSTAL STRUCTURE OF FMN QUINONE REDUCTASE 2 IN COMPLEX WITH RESVERATROL AT 1.85A

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)