5EA2

Crystal Structure of Holo NAD(P)H dehydrogenase, quinone 1

• PDB DOI: https://doi.org/10.2210/pdb5EA2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-15 Released: 2016-02-10 
• Deposition Author(s): Pidugu, L.S., Mbimba, J.E., Ahmad, M., Pozharski, E., Sausville, E.A., Emadi, A., Toth, E.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.216 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

A direct interaction between NQO1 and a chemotherapeutic dimeric naphthoquinone.

Pidugu, L.S., Mbimba, J.C., Ahmad, M., Pozharski, E., Sausville, E.A., Emadi, A., Toth, E.A.

(2016) BMC Struct Biol 16: 1-1

• PubMed: 26822308 
• DOI: https://doi.org/10.1186/s12900-016-0052-x
• Primary Citation of Related Structures:  
  5EA2, 5EAI


• PubMed Abstract: 
  

  Multimeric naphthoquinones are redox-active compounds that exhibit antineoplastic, antiprotozoal, and antiviral activities. Due to their multimodal effect on perturbation of cellular oxidative state, these compounds hold great potential as therapeutic agents against highly proliferative neoplastic cells. In our previous work, we developed a series of novel dimeric naphthoquinones and showed that they were selectively cytotoxic to human acute myeloid leukemia (AML), breast and prostate cancer cell lines. We subsequently identified the oxidoreductase NAD(P)H dehydrogenase, quinone 1 (NQO1) as the major target of dimeric naphthoquinones and proposed a mechanism of action that entailed induction of a futile redox cycling.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 127.43 kDa 
• Atom Count: 9,632 
• Modelled Residue Count: 1,090 
• Deposited Residue Count: 1,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H dehydrogenase [quinone] 1	A, B [auth C], C [auth E], D [auth G]	276	Homo sapiens	Mutation(s): 0  Gene Names: NQO1, DIA4, NMOR1 EC: 1.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P15559 (Homo sapiens) Explore P15559  Go to UniProtKB:  P15559
PHAROS:  P15559 GTEx:  ENSG00000181019

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], F [auth C], G [auth E], H [auth G]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.216 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.93	α = 90
b = 107.16	β = 100.68
c = 99.76	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Pidugu, L.S., Mbimba, J.E., Ahmad, M., Pozharski, E., Sausville, E.A., Emadi, A., Toth, E.A.

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Advisory, Data collection, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Advisory, Data collection, Database references, Refinement description