8W0J | pdb_00008w0j

Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with a propyne AMP ester inhibitor

PDB DOI: https://doi.org/10.2210/pdb8W0J/pdb

Classification: LIGASE
Organism(s): Candida albicans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-02-13 Released: 2024-02-21
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: 2.85 Å
R-Value Free:
0.226 (Depositor), 0.231 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.197 (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

Crystal structure of Acetyl-CoA synthetase 2 from Candida albicans in complex with a propyne AMP ester inhibitor

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

To be published.

Macromolecule Content

Total Structure Weight: 231.39 kDa
Atom Count: 14,241
Modeled Residue Count: 1,775
Deposited Residue Count: 2,058
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A synthetase 2	A, B, C	686	Candida albicans	Mutation(s): 1 Gene Names: ACS2 EC: 6.2.1.1
UniProt
Find proteins for Q8NJN3 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore Q8NJN3 Go to UniProtKB: Q8NJN3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NJN3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 AA [auth C] SDF format, chain D [auth A] SDF format, chain Q [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain D [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain D [auth A] mmCIF format, chain Q [auth B]	AA [auth C], D [auth A], Q [auth B]	5'-O-{(S)-hydroxy[(prop-2-yn-1-yl)oxy]phosphoryl}adenosine C₁₃ H₁₆ N₅ O₇ P JGOCYNVVFDYFDU-QYVSTXNMSA-N		Interactions Focus chain AA [auth C] Focus chain D [auth A] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth C] Focus chain D [auth A] Focus chain Q [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain T [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain T [auth B]	I [auth A], J [auth A], T [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain FA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain FA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain FA [auth C]	DA [auth C] EA [auth C] FA [auth C] K [auth A] L [auth A] DA [auth C], EA [auth C], FA [auth C], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	BA [auth C] CA [auth C] E [auth A] F [auth A] G [auth A] BA [auth C], CA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], R [auth B], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	U [auth B], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.226 (Depositor), 0.231 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.197 (Depositor)

Diffraction Data:

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.073	α = 90
b = 139.073	β = 90
c = 544.504	γ = 120

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-21

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	S10OD030394