9G5Y | pdb_00009g5y

The structure of Aspergillus fumigatus UDP-GlcNAc pyrophosphorylase in complex with a fragment

• PDB DOI: https://doi.org/10.2210/pdb9G5Y/pdb

• Classification: TRANSFERASE
• Organism(s): Aspergillus fumigatus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-17 Released: 2025-07-30 
• Deposition Author(s): Yan, K.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Exploration of starting points for the chemical validation of UDP-N-acetylglucosamine pyrophosphorylase in Aspergillus fumigatus

Yan, K., Stanley, M., Raimi, O., Kowalski, B., Gurvic, D., Grillenberger, S., Chen, X., Ferenbach, A.T., Dorfmueller, H., van Aalten, D.M.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 108.32 kDa 
• Atom Count: 7,543 
• Modeled Residue Count: 922 
• Deposited Residue Count: 968 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine diphosphorylase	A [auth B]	484	Aspergillus fumigatus	Mutation(s): 0  Gene Names: KXV57_008857 EC: 2.7.7.23
UniProt
Find proteins for A0A229XUD0 (Aspergillus fumigatus) Explore A0A229XUD0  Go to UniProtKB:  A0A229XUD0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine diphosphorylase	B [auth A]	484	Aspergillus fumigatus	Mutation(s): 0  Gene Names: KXV57_008857 EC: 2.7.7.23
UniProt
Find proteins for A0A229XUD0 (Aspergillus fumigatus) Explore A0A229XUD0  Go to UniProtKB:  A0A229XUD0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GN1	D [auth B]	2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose C8 H16 N O9 P FZLJPEPAYPUMMR-FMDGEEDCSA-N
A1IIG (Subject of Investigation/LOI)	E [auth B]	(3~{S})-3-azanyl-3-thiophen-2-yl-propanoic acid C7 H9 N O2 S GYAYLYLPTPXESE-YFKPBYRVSA-N
A1IIQ	C [auth B]	4-ethyl-2,5-dimethyl-pyrazol-3-amine C7 H13 N3 GUFRXHLYBBQWIV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM	A [auth B]	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.532	α = 90
b = 139.498	β = 90
c = 143.223	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Yan, K.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/V001094/1

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release