5V4P | pdb_00005v4p

Saccharomyces cerevisiae OYE 3 soaked with p-hydroxybenzaldehyde

• PDB DOI: https://doi.org/10.2210/pdb5V4P/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• 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., Powell III, R.W.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Saccharomyces cerevisiae OYE 3 soaked with p-hydroxybenzaldehyde

Stewart, J., Powell III, R.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.8 kDa 
• Atom Count: 6,847 
• Modeled Residue Count: 792 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], H [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
TOE	F [auth A], G [auth A], K [auth B], L [auth B]	2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL C7 H16 O4 JLGLQAWTXXGVEM-UHFFFAOYSA-N
HBA	D [auth A], I [auth B]	P-HYDROXYBENZALDEHYDE C7 H6 O2 RGHHSNMVTDWUBI-UHFFFAOYSA-N
NA	E [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.533	α = 90
b = 106.421	β = 90
c = 141.01	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., Powell III, R.W.

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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, Derived calculations