5N0F

The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with 1,6-ManSIFG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An atypical interaction explains the high-affinity of a non-hydrolyzable S-linked 1,6-alpha-mannanase inhibitor.

Belz, T.Jin, Y.Coines, J.Rovira, C.Davies, G.J.Williams, S.J.

(2017) Chem. Commun. (Camb.) 53: 9238-9241

  • DOI: 10.1039/c7cc04977c
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The non-hydrolyzable S-linked azasugars, 1,6-α-mannosylthio- and 1,6-α-mannobiosylthioisofagomine, were synthesized and shown to bind with high affinity to a family 76 endo-1,6-α-mannanase from Bacillus circulans. X-ray crystallography showed an atyp ...

    The non-hydrolyzable S-linked azasugars, 1,6-α-mannosylthio- and 1,6-α-mannobiosylthioisofagomine, were synthesized and shown to bind with high affinity to a family 76 endo-1,6-α-mannanase from Bacillus circulans. X-ray crystallography showed an atypical interaction of the isofagomine nitrogen with the catalytic acid/base. Molecular dynamics simulations reveal that the atypical binding results from sulfur perturbing the most stable form away from the nucleophile interaction preferred for the O-linked congener.


    Organizational Affiliation

    School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia. sjwill@unimelb.edu.au.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-1,6-mannanase
A, B
362Bacillus circulansMutation(s): 1 
Gene Names: aman6
Find proteins for Q9Z4P9 (Bacillus circulans)
Go to UniProtKB:  Q9Z4P9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7K2
Query on 7K2

Download SDF File 
Download CCD File 
A, B
(2~{R},3~{S},4~{S},5~{S},6~{R})-2-[[(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methylsulfanyl]-6-(hydroxymethyl)oxane-3,4,5-triol
C12 H23 N O7 S
KDPQETHZRPVZAI-TYMLGRTHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7K2Kd: 900 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.050α = 90.00
b = 86.400β = 90.00
c = 103.650γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ERCUnited KingdomAdG322942
Australian Research CouncilAustraliaFT130100103

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-08-16
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Database references