4AYQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.105 
  • R-Value Work: 0.088 
  • R-Value Observed: 0.089 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1002/anie.201205338
  • Primary Citation of Related Structures:  
    4AYO, 4AYP, 4AYQ, 4AYR

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE447Caulobacter sp. K31Mutation(s): 0 
EC: 3.2.1.113
UniProt
Find proteins for B0SWV2 (Caulobacter sp. (strain K31))
Explore B0SWV2 
Go to UniProtKB:  B0SWV2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0SWV2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MVL
Query on MVL

Download Ideal Coordinates CCD File 
E [auth A](5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL
C8 H12 N2 O4
RZRDQZQPTISYKY-JWXFUTCRSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MVL PDBBind:  4AYQ Kd: 47 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.105 
  • R-Value Work: 0.088 
  • R-Value Observed: 0.089 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.607α = 90
b = 143.607β = 90
c = 50.026γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description