5NZI

Crystal structure of UDP-glucose pyrophosphorylase S374F mutant from Leishmania major in complex with UDP-glucose

• PDB DOI: https://doi.org/10.2210/pdb5NZI/pdb

• Classification: TRANSFERASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-05-14 Released: 2018-04-18 
• Deposition Author(s): Cramer, J.T., Fuehring, J.I., Baruch, P., Bruetting, C., Hesse, R., Knoelker, H.-J., Gerardy-Schahn, R., Fedorov, R.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.244 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

Decoding Allosteric Networks in Biocatalysts: Rational Approach to Therapies and Biotechnologies

Cramer, J.T., Fuehring, J.I., Baruch, P., Bruetting, C., Knoelker, H.-J., Gerardy-Schahn, R., Fedorov, R.

(2018) ACS Catal 8

• DOI: https://doi.org/10.1021/acscatal.7b03714

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 56.87 kDa 
• Atom Count: 3,961 
• Modelled Residue Count: 482 
• 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): 1  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG	B [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.244 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.39	α = 90
b = 88.18	β = 90
c = 137.37	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SADABS	data scaling
AMoRE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Cramer, J.T., Fuehring, J.I., Baruch, P., Bruetting, C., Hesse, R., Knoelker, H.-J., Gerardy-Schahn, R., Fedorov, R.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	GZ: FE 1510/2-1

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.2: 2024-10-16
  Changes: Structure summary