5UX7 | pdb_00005ux7

Activated state yeast Glycogen Synthase in complex with UDP-xylose

• PDB DOI: https://doi.org/10.2210/pdb5UX7/pdb

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


• Deposited: 2017-02-22 Released: 2018-02-28 
• Deposition Author(s): Mahalingan, K.K., Hurley, T.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Activated state yeast Glycogen Synthase in complex with UDP-xylose

Mahalingan, K.K., Hurley, T.D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 330.2 kDa 
• Atom Count: 20,648 
• Modeled Residue Count: 2,550 
• Deposited Residue Count: 2,880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen [starch] synthase isoform 2	A, B, C, D	720	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: GSY2, YLR258W, L8479.8 EC: 2.4.1.11
UniProt
Find proteins for P27472 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27472  Go to UniProtKB:  P27472

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDX	G [auth B], I [auth C]	URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE C14 H22 N2 O16 P2 DQQDLYVHOTZLOR-OCIMBMBZSA-N
UDP	E [auth A], K [auth D]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
G6P	F [auth A], H [auth B], J [auth C], L [auth D]	6-O-phosphono-alpha-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-DVKNGEFBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.993	α = 90
b = 204.322	β = 90
c = 206.674	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Mahalingan, K.K., Hurley, T.D.

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Structure summary