2YDT

STRUCTURE OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A from FUSARIUM Graminearum in complexe with an iminosugar inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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: 10.1039/c1cc13675e
  • Primary Citation of Related Structures:  
    2YDP, 2YDT

  • 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASEA367Fusarium graminearumMutation(s): 0 
Gene Names: arb93a
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AHR
Query on AHR

Download Ideal Coordinates CCD File 
C [auth A]alpha-L-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-QMKXCQHVSA-N
 Ligand Interaction
EDG
Query on EDG

Download Ideal Coordinates CCD File 
B [auth A]1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL
C5 H11 N O3
OQEBIHBLFRADNM-YUPRTTJUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
N [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.435α = 90
b = 105.435β = 90
c = 140.038γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



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, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary