1GY8 | pdb_00001gy8

Trypanosoma brucei UDP-galactose 4' epimerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.245 (Depositor) 
  • R-Value Work: 
    0.216 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

High-Resolution Crystal Structure of Trypanosoma Brucei Udp-Galactose 4'-Epimerase: A Potential Target for Structure-Based Development of Novel Trypanocides

Shaw, M.P.Bond, C.S.Roper, J.R.Gourley, D.G.Ferguson, M.A.J.Hunter, W.N.

(2003) Mol Biochem Parasitol 126: 173

  • DOI: https://doi.org/10.1016/s0166-6851(02)00243-8
  • Primary Citation Related Structures: 
    1GY8

  • PubMed Abstract: 

    The crystal structure of UDP-galactose 4'-epimerase from the protozoan parasite Trypanosoma brucei in complex with the cofactor NAD(+) and a fragment of the substrates, UDP, has been determined at 2.0 A resolution (1 A = 0.1 nm). This enzyme, recently proven to be essential for this pathogenic parasite, shares 33% sequence identity with the corresponding enzyme in the human host. Structural comparisons indicate that many of the protein-ligand interactions are conserved between the two enzymes. However, in the UDP-binding pocket there is a non-conservative substitution from Gly237 in the human enzyme to Cys266 in the T. brucei enzyme. Such a significant difference could be exploited by the structure-based design of selective inhibitors using the structure of the trypanosomatid enzyme as a template.


  • Organizational Affiliation
    • Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.

Macromolecule Content 

  • Total Structure Weight: 179.5 kDa 
  • Atom Count: 12,972 
  • Modeled Residue Count: 1,467 
  • Deposited Residue Count: 1,588 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-GALACTOSE 4-EPIMERASE
A, B, C, D
397Trypanosoma bruceiMutation(s): 0 
EC: 5.1.3.2
UniProt
Find proteins for Q8T8E9 (Trypanosoma brucei)
Explore Q8T8E9 
Go to UniProtKB:  Q8T8E9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8T8E9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
UDP

Query on UDP



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.245 (Depositor) 
  • R-Value Work:  0.216 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.185α = 90
b = 112.533β = 90
c = 160.591γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description