5BXP

LNBase in complex with LNB-LOGNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis

Hattie, M.Ito, T.Debowski, A.W.Arakawa, T.Katayama, T.Yamamoto, K.Fushinobu, S.Stubbs, K.A.

(2015) Chem.Commun.(Camb.) 51: 15008-15011

  • DOI: 10.1039/c5cc05494j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The synthesis of potent inhibitors for lacto-N-biosidases and X-ray structural characterization of these compounds in complex with BbLNBase is described.

    The synthesis of potent inhibitors for lacto-N-biosidases and X-ray structural characterization of these compounds in complex with BbLNBase is described.


    Related Citations: 
    • Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum.
      Ito, T.,Katayama, T.,Hattie, M.,Sakurama, H.,Wada, J.,Suzuki, R.,Ashida, H.,Wakagi, T.,Yamamoto, K.,Stubbs, K.A.,Fushinobu, S.
      (2013) J. Biol. Chem. 288: 11795


    Organizational Affiliation

    School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia. keith.stubbs@uwa.edu.au.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lacto-N-biosidase
A, B
644Bifidobacterium bifidum JCM 1254Mutation(s): 0 
Gene Names: lnbB
Find proteins for B3TLD6 (Bifidobacterium bifidum JCM 1254)
Go to UniProtKB:  B3TLD6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
LOG
Query on LOG

Download SDF File 
Download CCD File 
A, B
LOGNAC
C8 H14 N2 O6
NJBKCLCEXIDHDR-OANDGCGGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 116.759α = 90.00
b = 131.617β = 90.00
c = 104.606γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-10-14
    Type: Database references