3L01

Crystal structure of monomeric glycogen synthase from Pyrococcus abyssi

• PDB DOI: https://doi.org/10.2210/pdb3L01/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus abyssi
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-12-09 Released: 2010-12-29 
• Deposition Author(s): Diaz, A., Martinez-Pons, C., Fita, I., Ferrer, J.C., Guinovart, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.3 kDa 
• Atom Count: 7,011 
• Modelled Residue Count: 856 
• Deposited Residue Count: 856 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GlgA glycogen synthase	A, B	428	Pyrococcus abyssi	Mutation(s): 1  Gene Names: PYRAB00770, PAB2292 EC: 2.4.1.21
UniProt
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2J8  Go to UniProtKB:  Q9V2J8

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	4		N/A
Glycosylation Resources
GlyTouCan:  G87171PZ GlyCosmos:  G87171PZ GlyGen:  G87171PZ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	K [auth A], L [auth A], S [auth B], T [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	E [auth A], F [auth A], G [auth A], M [auth B], N [auth B], O [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	H [auth A], I [auth A], J [auth A], P [auth B], Q [auth B], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900010	C, D	alpha-maltotetraose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.604	α = 90
b = 119.017	β = 90
c = 141.101	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-29 
Deposition Author(s): Diaz, A., Martinez-Pons, C., Fita, I., Ferrer, J.C., Guinovart, J.J.

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Structure summary
• Version 2.2: 2023-11-01
  Changes: Data collection, Refinement description