5NZH | pdb_00005nzh

Crystal structure of UDP-glucose pyrophosphorylase V402W mutant from Leishmania major

• PDB DOI: https://doi.org/10.2210/pdb5NZH/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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.269 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 112.28 kDa 
• Atom Count: 7,820 
• Modeled Residue Count: 965 
• Deposited Residue Count: 1,010 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose pyrophosphorylase	A, B	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.269 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.56	α = 90
b = 70.89	β = 123.54
c = 112.29	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.

---

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: 2018-10-24
  Changes: Advisory, Data collection, Derived calculations
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary