8YIE

Crystal structure of GH13_30 alpha-glucosidase CmmB in complex with acarbose

• PDB DOI: https://doi.org/10.2210/pdb8YIE/pdb

• Classification: HYDROLASE
• Organism(s): Arthrobacter globiformis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-29 Released: 2024-07-03 
• Deposition Author(s): Saburi, W., Tagami, T., Yu, J., Ose, T., Yao, M., Mori, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 

Starting Model: in silico

Literature

Molecular mechanism for the substrate specificity of Arthrobacter globiformis M6 alpha-glucosidase CmmB, belonging to glycoside hydrolase family 13 subfamily 30

Saburi, W., Tagami, T., Usui, T., Yu, J., Ose, T., Yao, M., Mori, H.

(2024) Food Biosci 61: 104516

• DOI: https://doi.org/10.1016/j.fbio.2024.104516

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 123.51 kDa 
• Atom Count: 9,354 
• Modelled Residue Count: 1,039 
• Deposited Residue Count: 1,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucosidase	A, B	550	Arthrobacter globiformis	Mutation(s): 0  Gene Names: cmmB EC: 3.2.1.20
UniProt
Find proteins for D2YYD7 (Arthrobacter globiformis) Explore D2YYD7  Go to UniProtKB:  D2YYD7

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)-alpha-D-glucopyranose	C, D	3	N/A	N/A
Glycosylation Resources
GlyTouCan:  G66431MI GlyCosmos:  G66431MI

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900007	C, D	alpha-acarbose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.364	α = 90
b = 66.19	β = 95.74
c = 148.06	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Saburi, W., Tagami, T., Yu, J., Ose, T., Yao, M., Mori, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release