4QOH

Crystal structure of fad quinone reductase 2 in complex with resveratrol at 1.6A

PDB DOI: https://doi.org/10.2210/pdb4QOH/pdb

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

Deposited: 2014-06-20 Released: 2015-07-01
Deposition Author(s): Serriere, J., Boutin, J.A., Isabet, T., Antoine, M., Ferry, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.238
R-Value Work: 0.202
R-Value Observed: 0.204

Starting Model: experimental
View more details

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 fad quinone reductase 2 in complex with resveratrol at 1.6A

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

To be published.

Macromolecule Content

Total Structure Weight: 54.21 kDa
Atom Count: 4,066
Modelled Residue Count: 457
Deposited Residue Count: 462
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD 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-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-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]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
STL	BindingDB: 4QOH	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: 1.60 Å
R-Value Free: 0.238
R-Value Work: 0.202
R-Value Observed: 0.204
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.69	α = 90
b = 82.27	β = 90
c = 106.13	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-07-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-01
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

4QOH

Crystal structure of fad quinone reductase 2 in complex with resveratrol at 1.6A

Crystal structure of fad quinone reductase 2 in complex with resveratrol at 1.6A

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)