4M28

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

• PDB DOI: https://doi.org/10.2210/pdb4M28/pdb

• Classification: TRANSFERASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-05 Released: 2014-01-29 
• Deposition Author(s): Fuehring, J.I., Routier, F.H., Lamerz, A.-C., Baruch, P., Gerardy-Schahn, R., Fedorov, R.

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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

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

• DOI: https://doi.org/10.1021/cs4007777

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.52 kDa 
• Atom Count: 3,834 
• Modelled Residue Count: 483 
• Deposited Residue Count: 505 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose pyrophosphorylase	A	505	Leishmania major	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPC	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 = 72.25	α = 90
b = 108.47	β = 90
c = 152.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
MxCuBE	data collection
XDS	data reduction
SADABS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Fuehring, J.I., Routier, F.H., Lamerz, A.-C., Baruch, P., Gerardy-Schahn, R., Fedorov, R.

Revision History  

• 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