2YDP

Structure of the E242A mutant of the alpha-l-arabinofuranosidase arb93a from fusarium graminearum in complex with an iminosugar inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history. 


Literature

Alpha-L-Arabinofuranosylated Pyrrolidines as Arabinanase Inhibitors.

Goddard-Borger, E.D., Carapito, R., Jeltsch, J., Phalip, V., Stick, R.V., Varrot, A.

(2011) Chem Commun (Camb) 47: 9684

  • DOI: https://doi.org/10.1039/c1cc13675e

  • PubMed Abstract: 

    As part of continued efforts to understand the mechanisms of 1,5-α-l-arabinanases better, some arabinan-like iminosugar oligosaccharides were synthesized. An iminosugar analogue of arabinobiose was found to be a good inhibitor of the arabinanase Arb93A from Fusarium graminearum. Structures were determined for complexes of this inhibitor with wild-type Arb93A and a catalytically inactive mutant.

    • Organizational Affiliation: 

    School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE
A, B, C
367Fusarium graminearumMutation(s): 1 
EC: 3.2.1.55
UniProt
Find proteins for B8ZY56 (Gibberella zeae)
Explore B8ZY56 
Go to UniProtKB:  B8ZY56
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8ZY56
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AHR
Query on AHR
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C]		alpha-L-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-QMKXCQHVSA-N
EDG
Query on EDG
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]		1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL
C5 H11 N O3
OQEBIHBLFRADNM-YUPRTTJUSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.93α = 90.14
b = 57.8β = 93.55
c = 91.6γ = 114.5
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 1.1: 2011-11-16
    Changes: Database references, Refinement description, Version format compliance
  • Version 1.2: 2015-04-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary