4AYR

Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with noeuromycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.102 
  • R-Value Work: 0.083 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Reaction Coordinate of a Bacterial Gh47 Alpha-Mannosidase: A Combined Quantum Mechanical and Structural Approach.

Thompson, A.J.Dabin, J.Iglesias-Fernandez, J.Ardevol, A.Dinev, Z.Williams, S.J.Bande, O.Siriwardena, A.Moreland, C.Hu, T.C.Smith, D.K.Gilbert, H.J.Rovira, C.Davies, G.J.

(2012) Angew.Chem.Int.Ed.Engl. 51: 10997

  • DOI: 10.1002/anie.201205338
  • Primary Citation of Related Structures:  4AYO, 4AYP, 4AYQ

  • PubMed Abstract: 
  • Mannosides in the southern hemisphere: Conformational analysis of enzymatic mannoside hydrolysis informs strategies for enzyme inhibition and inspires solutions to mannoside synthesis. Atomic resolution structures along the reaction coordinate of an ...

    Mannosides in the southern hemisphere: Conformational analysis of enzymatic mannoside hydrolysis informs strategies for enzyme inhibition and inspires solutions to mannoside synthesis. Atomic resolution structures along the reaction coordinate of an inverting α-mannosidase show how the enzyme distorts the substrate and transition state. QM/MM calculations reveal how the free energy landscape of isolated α-D-mannose is molded on enzyme to only allow one conformationally accessible reaction coordinate.


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE
A
447Caulobacter sp. (strain K31)EC: 3.2.1.113
Find proteins for B0SWV2 (Caulobacter sp. (strain K31))
Go to UniProtKB:  B0SWV2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

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Download CCD File 
A
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
POLYETHYLENE GLYCOL PEG4000
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
IFL
Query on IFL

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Download CCD File 
A
(3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE
ISOFAGOMINE LACTAM
C6 H11 N O4
ARBXEMIAJIJEQI-WDCZJNDASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IFLKd: 99 nM BINDINGMOAD
IFLKd: 99 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.102 
  • R-Value Work: 0.083 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 143.919α = 90.00
b = 143.919β = 90.00
c = 50.186γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-30
    Type: Initial release