5ZCE

Crystal structure of Alpha-glucosidase in complex with maltotetraose

• PDB DOI: https://doi.org/10.2210/pdb5ZCE/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. (in: firmicutes)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-16 Released: 2018-12-26 
• Deposition Author(s): Kato, K., Saburi, W., Yao, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.191 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 65.72 kDa 
• Atom Count: 5,359 
• Modelled Residue Count: 545 
• Deposited Residue Count: 555 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucosidase	A	555	Bacillus sp. (in: firmicutes)	Mutation(s): 0
UniProt
Find proteins for A0A2Z5WH92 (Bacillus sp) Explore A0A2Z5WH92  Go to UniProtKB:  A0A2Z5WH92

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	B	4		N/A
Glycosylation Resources
GlyTouCan:  G87171PZ GlyCosmos:  G87171PZ GlyGen:  G87171PZ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], 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_900010	B	alpha-maltotetraose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.191 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.989	α = 90
b = 84.549	β = 90
c = 128.715	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Kato, K., Saburi, W., Yao, M.

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary