6N1E

Crystal structure of X. citri phosphoglucomutase in complex with 1-methyl-glucose 6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


Literature

Synthesis, Derivatization, and Structural Analysis of Phosphorylated Mono-, Di-, and Trifluorinated d-Gluco-heptuloses by Glucokinase: Tunable Phosphoglucomutase Inhibition.

Zhu, J.S.Stiers, K.M.Winter, S.M.Garcia, A.D.Versini, A.F.Beamer, L.J.Jakeman, D.L.

(2019) ACS Omega 4: 7029-7037

  • DOI: https://doi.org/10.1021/acsomega.9b00008
  • Primary Citation of Related Structures:  
    6N1E

  • PubMed Abstract: 

    Glucokinase phosphorylated a series of C-1 fluorinated α-d-gluco-heptuloses. These phosphorylated products were discovered to be inhibitors of α-phosphomannomutase/phosphoglucomutase (αPMM/PGM) and β-phosphoglucomutase (βPGM). Inhibition potency with both mutases inversely correlated to the degree of fluorination. Structural analysis with αPMM demonstrated the inhibitor binding to the active site, with the phosphate in the phosphate binding site and the anomeric hydroxyl directed to the catalytic site.


  • Organizational Affiliation

    Department of Chemistry, Hogeschool Leiden (UAS Leiden), Zernikedreef 11, CK Leiden 2333, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphomannomutase/phosphoglucomutase468Xanthomonas citriMutation(s): 0 
Gene Names: xavtCFBP7764_14885
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QIF (Subject of Investigation/LOI)
Query on QIF

Download Ideal Coordinates CCD File 
C [auth A]1-deoxy-7-O-phosphono-alpha-D-gluco-hept-2-ulopyranose
C7 H15 O9 P
DFHDZDLZUMUBKN-ZFYZTMLRSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.705α = 90
b = 54.745β = 90
c = 172.432γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary