5BUC | pdb_00005buc

Oxidized quinone reductase 2 in complex with ethidium

PDB DOI: https://doi.org/10.2210/pdb5BUC/pdb

Classification: Oxidoreductase/oxidoreductase Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-06-03 Released: 2016-06-15
Deposition Author(s): Leung, K.K., Shilton, B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.199 (Depositor), 0.200 (DCC)
R-Value Work:
0.153 (Depositor), 0.160 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of quinone reductase 2 in complex with DNA intercalating agents

Leung, K.K., Shilton, B.H.

To be published.

Macromolecule Content

Total Structure Weight: 54.44 kDa
Atom Count: 4,261
Modeled Residue Count: 460
Deposited Residue Count: 460
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	230	Homo sapiens	Mutation(s): 0 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 D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
ET Query on ET Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	E [auth A], F [auth A], H [auth B]	ETHIDIUM C₂₁ H₂₀ N₃ QTANTQQOYSUMLC-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.199 (Depositor), 0.200 (DCC)
R-Value Work: 0.153 (Depositor), 0.160 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.81	α = 90
b = 82.85	β = 90
c = 106.43	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-06-15

Deposition Author(s):

Leung, K.K.

Shilton, B.H.

Revision History (Full details and data files)

Version 1.0: 2016-06-15
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description

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Help and Resources

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Oxidized quinone reductase 2 in complex with ethidium

Structure of quinone reductase 2 in complex with DNA intercalating agents

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations