5V4V | pdb_00005v4v

Saccharomyces cerevisiae Old Yellow Enzyme 3

• PDB DOI: https://doi.org/10.2210/pdb5V4V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-10 Released: 2018-03-14 
• Deposition Author(s): Stewart, J.D.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Saccharomyces cerevisiae Old Yellow Enzyme 3

Stewart, J.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 91.28 kDa 
• Atom Count: 7,418 
• Modeled Residue Count: 794 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH dehydrogenase 3	A, B	400	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: OYE3, YPL171C, P2291 EC: 1.6.99.1
UniProt
Find proteins for P41816 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41816  Go to UniProtKB:  P41816

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
NCA	D [auth A], G [auth B]	NICOTINAMIDE C6 H6 N2 O DFPAKSUCGFBDDF-UHFFFAOYSA-N
GOL	E [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.214	α = 90
b = 107.762	β = 90
c = 141.071	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Stewart, J.D.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1111791

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references