3UPW | pdb_00003upw

Pichia Stipitis OYE2.6 complexed with nicotinamide

• PDB DOI: https://doi.org/10.2210/pdb3UPW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Scheffersomyces stipitis CBS 6054
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-18 Released: 2012-07-11 
• Deposition Author(s): Pompeu, Y.A., Stewart, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions

Pompeu, Y.A., Sullivan, B., Walton, A.Z., Stewart, J.D.

(2012) Adv Synth Catal 

• DOI: https://doi.org/10.1002/adsc.201200213

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)

Macromolecule Content 

• Total Structure Weight: 46.28 kDa 
• Atom Count: 3,721 
• Modeled Residue Count: 404 
• Deposited Residue Count: 407 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase	A	407	Scheffersomyces stipitis CBS 6054	Mutation(s): 0  Gene Names: OYE2.6, PICST_44614 EC: 1.6.99.1
UniProt
Find proteins for A3LT82 (Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545)) Explore A3LT82  Go to UniProtKB:  A3LT82

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
NCA	F [auth A]	NICOTINAMIDE C6 H6 N2 O DFPAKSUCGFBDDF-UHFFFAOYSA-N
MLA	C [auth A], D [auth A], E [auth A]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
NA	G [auth A], H [auth A], I [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.306	α = 90
b = 127.306	β = 90
c = 123.064	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Pompeu, Y.A., Stewart, J.D.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Non-polymer description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description