1OD8

Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine lactam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.126 
  • R-Value Work: 0.103 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Xylobiose-Derived Isofagomine Lactam Glycosidase Inhibitor Binds as its Amide Tautomer

Gloster, T.M.Williams, S.J.Tarling, C.Roberts, S.Dupont, C.Jodoin, P.Shareck, F.Withers, S.G.Davies, G.J.

(2003) Chem.Commun.(Camb.) 8: 944


  • PubMed Abstract: 
  • The atomic-resolution structure of a xylobiose-derived isofagomine lactam in complex with the xylanase Xyn10A from Streptomyces lividans reveals that the lactam is bound to the enzyme as the amide tautomer, with "reversed" protonation-states for nucl ...

    The atomic-resolution structure of a xylobiose-derived isofagomine lactam in complex with the xylanase Xyn10A from Streptomyces lividans reveals that the lactam is bound to the enzyme as the amide tautomer, with "reversed" protonation-states for nucleophile and acid-base.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-BETA-XYLANASE A
A
313Streptomyces lividansGene Names: xlnA
EC: 3.2.1.8
Find proteins for P26514 (Streptomyces lividans)
Go to UniProtKB:  P26514
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XDL
Query on XDL

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Download CCD File 
A
XYLOSE-DERIVED ISOFAGOMINE LACTAM
(3S)-3-HYDROXYPIPERIDIN-2-ONE
C5 H9 N O2
RYKLZUPYJFFNRR-BYPYZUCNSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
XYP
Query on XYP

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Download CCD File 
A
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.126 
  • R-Value Work: 0.103 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.814α = 90.00
b = 45.878β = 90.00
c = 85.737γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance