4M28

UDP-Glucose Pyrophosphorylase from Leishmania major in complex with UTP analog dUpCpp

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Catalytic mechanism and allosteric regulation of UDP-glucose pyrophosphorylase from Leishmania major

Fuehring, J.I., Routier, F.H., Lamerz, A.-C., Baruch, P., Gerardy-Schahn, R., Fedorov, R.

(2013) ACS Catal 3: 2976-2985


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-glucose pyrophosphorylase505Leishmania majorMutation(s): 0 
Gene Names: UGP, LMJF_18_0990
EC: 2.7.7.9
UniProt
Find proteins for Q4QDU3 (Leishmania major)
Explore Q4QDU3 
Go to UniProtKB:  Q4QDU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QDU3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UPC
Query on UPC
Download Ideal Coordinates CCD File 
B [auth A]2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine
C10 H17 N2 O13 P3
CLYYXAGDTAZMBH-LKEWCRSYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.25α = 90
b = 108.47β = 90
c = 152.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
MxCuBEdata collection
XDSdata reduction
SADABSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary