9G53 | pdb_00009g53

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

PDB DOI: https://doi.org/10.2210/pdb9G53/pdb

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

Deposited: 2024-07-16 Released: 2025-07-30
Deposition Author(s): Yan, K.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.263 (Depositor), 0.264 (DCC)
R-Value Work:
0.216 (Depositor), 0.217 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 216.77 kDa
Atom Count: 15,150
Modeled Residue Count: 1,874
Deposited Residue Count: 1,936
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine diphosphorylase	A [auth B], 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A229XUD0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine diphosphorylase	C, D	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A229XUD0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GN1 Query on GN1 Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain I [auth A] MOL2 format, chain E [auth B] MOL2 format, chain I [auth A] mmCIF format, chain E [auth B] mmCIF format, chain I [auth A]	E [auth B], I [auth A]	2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose C₈ H₁₆ N O₉ P FZLJPEPAYPUMMR-FMDGEEDCSA-N		Interactions Focus chain E [auth B] Focus chain I [auth A] Interactions & Density Focus chain E [auth B] Focus chain I [auth A]
71G Query on 71G Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain G [auth B] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] mmCIF format, chain G [auth B] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D]	G [auth B], L [auth D], M [auth D]	3-aminobenzonitrile C₇ H₆ N₂ NJXPYZHXZZCTNI-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain G [auth B] Focus chain L [auth D] Focus chain M [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]