8G0V | pdb_00008g0v

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

PDB DOI: https://doi.org/10.2210/pdb8G0V/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.173 (Depositor), 0.170 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 233.86 kDa
Atom Count: 16,338
Modeled Residue Count: 1,996
Deposited Residue Count: 2,082
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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 (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VFT1 Go to UniProtKB: J9VFT1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J9VFT1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YHT (Subject of Investigation/LOI) Query on YHT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C]	E [auth A], I [auth B], J [auth C]	5'-O-{(S)-hydroxy[(prop-2-yn-1-yl)oxy]phosphoryl}adenosine C₁₃ H₁₆ N₅ O₇ P JGOCYNVVFDYFDU-QYVSTXNMSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C]
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.173 (Depositor), 0.170 (DCC)
R-Value Observed: 0.174 (Depositor)

Diffraction Data: https://doi.org/10.18430/M38G0V

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.079	α = 70.11
b = 81.827	β = 74.37
c = 101.32	γ = 88.37

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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)

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