2Y5E

BARLEY LIMIT DEXTRINASE IN COMPLEX WITH ALPHA-CYCLODEXTRIN

• PDB DOI: https://doi.org/10.2210/pdb2Y5E/pdb
• Entry: 2Y5E supersedes: 2X4C

• Classification: HYDROLASE
• Organism(s): Hordeum vulgare
• Expression System: Komagataella phaffii GS115
• Mutation(s): Yes 


• Deposited: 2011-01-13 Released: 2011-01-26 
• Deposition Author(s): Vester-Christensen, M.B., Hachem, M.A., Svensson, B., Henriksen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.226 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 99.62 kDa 
• Atom Count: 6,986 
• Modelled Residue Count: 866 
• Deposited Residue Count: 884 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIMIT DEXTRINASE	A	884	Hordeum vulgare	Mutation(s): 3  EC: 3.2.1.41
UniProt
Find proteins for O48541 (Hordeum vulgare subsp. vulgare) Explore O48541  Go to UniProtKB:  O48541

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
Cyclohexakis-(1-4)-(alpha-D-glucopyranose)	B	6		N/A
Glycosylation Resources
GlyTouCan:  G22307HL GlyCosmos:  G22307HL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900015	B	alpha-cyclodextrin	Oligosaccharide / Drug delivery

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.226 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.84	α = 90
b = 85.61	β = 96.83
c = 61.12	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-26 
Deposition Author(s): Vester-Christensen, M.B., Hachem, M.A., Svensson, B., Henriksen, A.
• This entry supersedes: 2X4C

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2012-11-21
  Changes: Database references, Non-polymer description
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: 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