6UHX

Crystal structure of YIR035C short chain dehydrogenases/reductase from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb6UHX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-09-29 Released: 2020-08-05 
• Deposition Author(s): Stogios, P.J., Skarina, T., Chen, C., Kagan, O., Iakounine, A., Savchenko, A.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.315 
• R-Value Work: 0.235 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

Crystal structure of YIR035C short chain dehydrogenases/reductase from Saccharomyces cerevisiae

Chen, C.

To be published.

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: 56.5 kDa 
• Atom Count: 4,058 
• Modelled Residue Count: 507 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized oxidoreductase YIR035C	A, B	254	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YIR035C EC: 1
UniProt
Find proteins for P40579 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40579  Go to UniProtKB:  P40579

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.315 
• R-Value Work: 0.235 
• R-Value Observed: 0.239 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.545	α = 90
b = 73.049	β = 100.137
c = 67.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
Coot	model building
PHENIX	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Stogios, P.J., Skarina, T., Chen, C., Kagan, O., Iakounine, A., Savchenko, A.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	Industrial Biocatalysis Network

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description