4FGJ | pdb_00004fgj

Oxidized quinone reductase 2 in complex with primaquine

PDB DOI: https://doi.org/10.2210/pdb4FGJ/pdb

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

Deposited: 2012-06-04 Released: 2013-03-13
Deposition Author(s): Leung, K.K., Shilton, B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.167 (Depositor), 0.169 (DCC)
R-Value Work:
0.141 (Depositor), 0.142 (DCC)
R-Value Observed:
0.142 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structures of quinone reductase 2 bound to antimalarial drugs reveal conformational change upon reduction

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

(2013) J Biological Chem

Macromolecule Content

Total Structure Weight: 54.62 kDa
Atom Count: 4,436
Modeled Residue Count: 460
Deposited Residue Count: 466
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosyldihydronicotinamide dehydrogenase [quinone]	A, B	233	Homo sapiens	Mutation(s): 0 Gene Names: NMOR2, NQO2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
1PQ Query on 1PQ Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	(4S)-N~4~-(6-methoxyquinolin-8-yl)pentane-1,4-diamine C₁₅ H₂₁ N₃ O INDBQLZJXZLFIT-NSHDSACASA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth B] MOL2 format, chain G [auth B] MOL2 format, chain J [auth B] mmCIF format, chain G [auth B] mmCIF format, chain J [auth B]	G [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth B] Interactions & Density Focus chain G [auth B] Focus chain J [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.167 (Depositor), 0.169 (DCC)
R-Value Work: 0.141 (Depositor), 0.142 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.5	α = 90
b = 83	β = 90
c = 106.49	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxDC	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-03-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-03-13
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.