8EPS | pdb_00008eps

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

PDB DOI: https://doi.org/10.2210/pdb8EPS/pdb

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

Deposited: 2022-10-06 Released: 2022-10-19
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.236 (Depositor), 0.230 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (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

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

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

To be published.

Macromolecule Content

Total Structure Weight: 233.59 kDa
Atom Count: 15,277
Modeled Residue Count: 1,948
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WPO (Subject of Investigation/LOI) Query on WPO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	5'-O-{(S)-hydroxy[(prop-2-en-1-yl)oxy]phosphoryl}adenosine C₁₃ H₁₈ N₅ O₇ P LNGYCTNQUWBENP-QYVSTXNMSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.236 (Depositor), 0.230 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.179 (Depositor)

Diffraction Data: https://doi.org/10.18430/M38EPS

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.138	α = 66.22
b = 86.889	β = 73.16
c = 105.861	γ = 89.32

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-10-19

Deposition Author(s):

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	HHSN272201700059C

Revision History (Full details and data files)

Version 1.0: 2022-10-19
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-22
Changes: Data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.