4BQF

Arabidopsis thaliana cytosolic alpha-1,4-glucan phosphorylase (PHS2) in complex with acarbose

• PDB DOI: https://doi.org/10.2210/pdb4BQF/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-30 Released: 2014-02-19 
• Deposition Author(s): O'Neill, E.C., Rashid, A.M., Stevenson, C.E.M., Hetru, A.C., Gunning, A.P., Rejzek, M., Nepogodiev, S.A., Bornemann, S., Lawson, D.M., Field, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Sugar-Coated Sensor Chip and Nanoparticle Surfaces for the in Vitro Enzymatic Synthesis of Starch-Like Materials

O'Neill, E.C., Rashid, A.M., Stevenson, C.E.M., Hetru, A.C., Gunning, A.P., Rejzek, M., Nepogodiev, S.A., Bornemann, S., Lawson, D.M., Field, R.A.

(2014) Chem Sci 5: 341

• DOI: https://doi.org/10.1039/C3SC51829A

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: 200.55 kDa 
• Atom Count: 13,573 
• Modelled Residue Count: 1,651 
• Deposited Residue Count: 1,748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-GLUCAN PHOSPHORYLASE 2, CYTOSOLIC	A, B	874	Arabidopsis thaliana	Mutation(s): 0  EC: 2.4.1.1
UniProt
Find proteins for Q9SD76 (Arabidopsis thaliana) Explore Q9SD76  Go to UniProtKB:  Q9SD76

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	C, D	3	N/A	N/A
Glycosylation Resources
GlyTouCan:  G08743RW GlyCosmos:  G08743RW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], H [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GLC	F [auth A], G [auth A], I [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
GOL	J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900022	C, D	beta-acarbose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.249	α = 90
b = 117.075	β = 106.79
c = 94.967	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): O'Neill, E.C., Rashid, A.M., Stevenson, C.E.M., Hetru, A.C., Gunning, A.P., Rejzek, M., Nepogodiev, S.A., Bornemann, S., Lawson, D.M., Field, R.A.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary