6F9H

Crystal structure of Barley Beta-Amylase complexed with 4-S-alpha-D-glucopyranosyl-(1,4-dideoxy-4-thio-nojirimycin)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Synthesis, biological and structural analysis of prospective glycosyl-iminosugar prodrugs: impact on germination

Moncayo, M.A.Rodrigues, L.L.Stevenson, C.E.M.Ruzanski, C.Rejzek, M.Lawson, D.M.Angulo, J.Field, R.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-amylaseA535Hordeum vulgareMutation(s): 1 
Gene Names: Bmy1
EC: 3.2.1.2
Find proteins for A8CFR3 (Hordeum vulgare)
Explore A8CFR3 
Go to UniProtKB:  A8CFR3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download CCD File 
A
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
SGJ
Query on SGJ

Download CCD File 
A
1,4-dideoxy-4-thio-nojirimycin
C6 H13 N O3 S
NSHHSUUKQHDEOL-JGWLITMVSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.52α = 90
b = 99.11β = 90
c = 65.04γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
BBSRC Institute Strategic Programme on Understanding and Exploiting Metabolism (MET)United KingdomBB/J004561/1
John Innes FoundationUnited Kingdom--
Royal Society Newton Fund FellowshipUnited Kingdom--

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary