5L7V

Crystal Structure of BvGH123 with bond transition state analog Galthiazoline.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GNLClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structural and mechanistic insights into a Bacteroides vulgatus retaining N-acetyl-beta-galactosaminidase that uses neighbouring group participation.

Roth, C.Petricevic, M.John, A.Goddard-Borger, E.D.Davies, G.J.Williams, S.J.

(2016) Chem Commun (Camb) 52: 11096-11099

  • DOI: https://doi.org/10.1039/c6cc04649e
  • Primary Citation of Related Structures:  
    5L7R, 5L7U, 5L7V

  • PubMed Abstract: 

    Bacteroides vulgatus is a member of the human microbiota whose abundance is increased in patients with Crohn's disease. We show that a B. vulgatus glycoside hydrolase from the carbohydrate active enzyme family GH123, BvGH123, is an N-acetyl-β-galactosaminidase that acts with retention of stereochemistry, and, through a 3-D structure in complex with Gal-thiazoline, provide evidence in support of a neighbouring group participation mechanism.


  • Organizational Affiliation

    Department of Chemistry, University of York, Heslington, York, UK. gideon.davies@york.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
glycoside hydrolase
A, B
563Phocaeicola vulgatus ATCC 8482Mutation(s): 0 
Gene Names: BVU_2198
UniProt
Find proteins for A6L2E5 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154))
Explore A6L2E5 
Go to UniProtKB:  A6L2E5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6L2E5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNL
Query on GNL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol
C8 H13 N O4 S
DRHXTSWSUAJOJZ-JAJWTYFOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.504α = 90
b = 148.386β = 90
c = 147.659γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GNLClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary