8YIE | pdb_00008yie

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.203 (Depositor), 0.203 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2YYD7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
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 Query on PRD_900007	C, D	alpha-acarbose	Oligosaccharide / Inhibitor		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203 (Depositor), 0.203 (DCC)
R-Value Work: 0.165 (Depositor), 0.165 (DCC)
R-Value Observed: 0.165 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.