6LX1

Potato D-enzyme complexed with Acarbose

• PDB DOI: https://doi.org/10.2210/pdb6LX1/pdb

• Classification: TRANSFERASE
• Organism(s): Solanum tuberosum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-10 Released: 2020-08-26 
• Deposition Author(s): Unno, H., Imamura, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.206 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

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)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 59.94 kDa 
• Atom Count: 4,621 
• Modelled Residue Count: 515 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-alpha-glucanotransferase, chloroplastic/amyloplastic	A	524	Solanum tuberosum	Mutation(s): 0  Gene Names: DPEP EC: 2.4.1.25
UniProt
Find proteins for Q06801 (Solanum tuberosum) Explore Q06801  Go to UniProtKB:  Q06801

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)-1,5-anhydro-D-glucitol	B	2	N/A	N/A
Glycosylation Resources
GlyTouCan:  G87323JT GlyCosmos:  G87323JT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.206 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.171	α = 90
b = 120.293	β = 90
c = 174.698	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Unno, H., Imamura, K.

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references
• Version 1.2: 2020-10-07
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Database references, Refinement description