5M77

a GH76 family enzyme structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.121 

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
589Bacillus circulansMutation(s): 1 
Gene Names: aman6
Find proteins for Q9Z4P9 (Bacillus circulans)
Go to UniProtKB:  Q9Z4P9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7K3
Query on 7K3

Download SDF File 
Download CCD File 
A, B
(2~{R},3~{S},4~{S},5~{S},6~{R})-2-(hydroxymethyl)-6-sulfanyl-oxane-3,4,5-triol
C6 H12 O5 S
JUSMHIGDXPKSID-RWOPYEJCSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.060α = 90.00
b = 85.170β = 90.00
c = 101.860γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
xia2data reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ERCUnited KingdomAdG-322942

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