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 
  • R-Value Observed: 0.104 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 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

  • DOI: https://doi.org/10.1039/b301829f
  • Primary Citation of Related Structures:  
    1OD8

  • 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 nucleophile and acid-base.

    • Organizational Affiliation: 

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


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENDO-1,4-BETA-XYLANASE A313Streptomyces lividansMutation(s): 0 
EC: 3.2.1.8
UniProt
Find proteins for P26514 (Streptomyces lividans)
Explore P26514 
Go to UniProtKB:  P26514
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26514
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XYP
Query on XYP
Download Ideal Coordinates CCD File 
F [auth A],
J [auth A]		beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
XDL
Query on XDL
Download Ideal Coordinates CCD File 
E [auth A],
I [auth A]		XYLOSE-DERIVED ISOFAGOMINE LACTAM
C5 H9 N O2
RYKLZUPYJFFNRR-BYPYZUCNSA-N
IMD
Query on IMD
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]		IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
NA
Query on NA
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
K [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.126 
  • R-Value Work: 0.103 
  • R-Value Observed: 0.104 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.814α = 90
b = 45.878β = 90
c = 85.737γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary