8TG2 | pdb_00008tg2

The crystal structure of the post-reactive state of UDP-sugar pyrophosphorylase from Leishmania major in complex with products UDP-Glucose and PPi

• PDB DOI: https://doi.org/10.2210/pdb8TG2/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-12 Released: 2025-02-12 
• Deposition Author(s): Prakash, O., Fuehring, J.I., Baruch, P., Routier, F.H., Fedorov, R.
• Funding Organization(s): German Research Foundation (DFG), European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

The post-reactive state structures of Leishmania major UDP-sugar pyrophosphorylase provide insights into the product release mechanism

Prakash, O., Fuehring, J.I., Baruch, P., Routier, F.H., Fedorov, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.85 kDa 
• Atom Count: 4,969 
• Modeled Residue Count: 608 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UTP-monosaccharide-1-phosphate uridylyltransferase	A	608	Leishmania major	Mutation(s): 0  Gene Names: USP EC: 2.7.7.64
UniProt
Find proteins for D3G6S4 (Leishmania major) Explore D3G6S4  Go to UniProtKB:  D3G6S4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG (Subject of Investigation/LOI)	B [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
POP (Subject of Investigation/LOI)	C [auth A], D [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.09	α = 90
b = 121.9	β = 105.69
c = 60.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Prakash, O., Fuehring, J.I., Baruch, P., Routier, F.H., Fedorov, R.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FE 1510/2-1
European Union (EU)	European Union	EU FP7, GA. 608295

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release