6G9V | pdb_00006g9v

Crystal structure of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase(AfUAP1) in complex with UDPGlcNAc, pyrophosphate and Mg2+

PDB DOI: https://doi.org/10.2210/pdb6G9V/pdb

Classification: TRANSFERASE
Organism(s): Aspergillus fumigatus Af293
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-11 Released: 2019-04-24
Deposition Author(s): Raimi, O.G., Hurtado-Guerrero, R., Borodin, V., Urbaniak, M., Ferguson, M., van Aalten, D.
Funding Organization(s): Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.240 (Depositor), 0.239 (DCC)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A mechanism-inspired UDP-N-acetylglucosamine pyrophosphorylase inhibitor

Raimi, O.G., Hurtado-Guerrero, R., Borodkin, V., Ferenbach, A., Urbaniak, M.D., Ferguson, M.A.J., van Aalten, D.M.F.

(2020) RSC Chem Biol

DOI: https://doi.org/10.1039/C9CB00017H

Macromolecule Content

Total Structure Weight: 114.4 kDa
Atom Count: 7,902
Modeled Residue Count: 925
Deposited Residue Count: 1,018
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine pyrophosphorylase	A, B	509	Aspergillus fumigatus Af293	Mutation(s): 0 Gene Names: AFUA_7G02180 EC: 2.7.7.23
UniProt
Find proteins for Q4WAR0 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WAR0 Go to UniProtKB: Q4WAR0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4WAR0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UD1 Query on UD1 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C₁₇ H₂₇ N₃ O₁₇ P₂ LFTYTUAZOPRMMI-CFRASDGPSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
PPV Query on PPV Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.240 (Depositor), 0.239 (DCC)
R-Value Work: 0.207 (Depositor)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.195	α = 90
b = 139.839	β = 90
c = 144.615	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-04-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	M004139

Revision History (Full details and data files)

Version 1.0: 2019-04-24
Type: Initial release
Version 1.1: 2020-04-01
Changes: Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description