4YNC

OYE1 W116A COMPLEXED WITH (Z)-METHYL-3-CYANO-3-PHENYLACRYLATE IN A NON PRODUCTIVE BINDING MODE

• PDB DOI: https://doi.org/10.2210/pdb4YNC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces pastorianus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-03-09 Released: 2016-01-20 
• Deposition Author(s): Santangelo, S., Brenna, E., Stewart, J.D., Powell III, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.172 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

Starting Model: experimental

Literature

Opposite Enantioselectivity in the Bioreduction of (Z)-beta-Aryl-beta-cyanoacrylates Mediated by the Tryptophan 116 Mutants of Old Yellow Enzyme 1: Synthetic Approach to (R)- and (S)-beta-Aryl-gamma-lactams

Brenna, E., Crotti, M., Gatti, F.G., Monti, D., Parmeggiani, F., Powell III, R.W., Santangelo, S., Stewart, J.D.

(2015) Adv Synth Catal 357: 1849-1860.

• DOI: https://doi.org/10.1002/adsc.201500206

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 45.25 kDa 
• Atom Count: 3,851 
• Modelled Residue Count: 397 
• Deposited Residue Count: 397 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH dehydrogenase 1	A	397	Saccharomyces pastorianus	Mutation(s): 1  Gene Names: OYE1 EC: 1.6.99.1
UniProt
Find proteins for Q02899 (Saccharomyces pastorianus) Explore Q02899  Go to UniProtKB:  Q02899

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
4EG	C [auth A]	methyl (2Z)-3-cyano-3-phenylprop-2-enoate C11 H9 N O2 GXUWXZSLWMEZET-JXMROGBWSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.172 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.503	α = 90
b = 141.503	β = 90
c = 42.868	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Santangelo, S., Brenna, E., Stewart, J.D., Powell III, R.W.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 2.0: 2024-01-10
  Changes: Atomic model, Data collection, Database references, Refinement description