8G0U

Crystal Structure of Acetyl-CoA synthetase in complex with an isopropyl ester AMP inhibitor from Cryptococcus neoformans H99

• PDB DOI: https://doi.org/10.2210/pdb8G0U/pdb

• Classification: LIGASE
• Organism(s): Cryptococcus neoformans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-02-01 Released: 2023-02-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Starting Model: experimental

Literature

Crystal Structure of Acetyl-CoA synthetase in complex with an isopropyl ester AMP inhibitor from Cryptococcus neoformans H99

Liu, L., Lovell, S., Battaile, K.P., Staker, B.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 233.97 kDa 
• Atom Count: 15,010 
• Modelled Residue Count: 1,784 
• Deposited Residue Count: 2,082 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A synthetase	A, B, C	694	Cryptococcus neoformans	Mutation(s): 0  EC: 6.2.1.1
UniProt
Find proteins for J9VFT1 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VFT1  Go to UniProtKB:  J9VFT1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YHQ (Subject of Investigation/LOI)	F [auth A], I [auth B], L [auth C]	5'-O-{(R)-hydroxy[(propan-2-yl)oxy]phosphoryl}adenosine C13 H20 N5 O7 P UCVFYZHKFZWYCU-QYVSTXNMSA-N
EDO	D [auth A], E [auth A], G [auth B], H [auth B], J [auth C], K [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M38G0U

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.879	α = 90
b = 183.779	β = 92.98
c = 84.076	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	OD030394

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection