7KQ6 | pdb_00007kq6

Crystal Structure of Acetyl-coenzyme A synthetase from Coccidioides immitis in complex with PRX

PDB DOI: https://doi.org/10.2210/pdb7KQ6/pdb

Classification: LIGASE
Organism(s): Coccidioides immitis RS
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-11-13 Released: 2020-12-09
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.185 (Depositor), 0.186 (DCC)
R-Value Work:
0.162 (Depositor)
R-Value Observed:
0.162 (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-coenzyme A synthetase synthetase from Coccidioides immitis in complex with PRX

DeBouver, N.D., Fox III, D., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 238.46 kDa
Atom Count: 15,819
Modeled Residue Count: 1,808
Deposited Residue Count: 2,118
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	A, B, C	706	Coccidioides immitis RS	Mutation(s): 0 Gene Names: CIMG_01510 EC: 6.2.1.1
UniProt
Find proteins for J3KJC6 (Coccidioides immitis (strain RS)) Explore J3KJC6 Go to UniProtKB: J3KJC6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J3KJC6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRX (Subject of Investigation/LOI) Query on PRX Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain D [auth A] SDF format, chain N [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B]	CA [auth C], D [auth A], N [auth B]	ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER C₁₃ H₂₀ N₅ O₇ P XAMXMSZRQHPMRX-QYVSTXNMSA-N		Interactions Focus chain CA [auth C] Focus chain D [auth A] Focus chain N [auth B] Interactions & Density Focus chain CA [auth C] Focus chain D [auth A] Focus chain N [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain I [auth A] SDF format, chain HA [auth C] SDF format, chain H [auth A] SDF format, chain GA [auth C] SDF format, chain G [auth A] SDF format, chain FA [auth C] SDF format, chain F [auth A] SDF format, chain EA [auth C] SDF format, chain E [auth A] SDF format, chain DA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth C] DA [auth C] E [auth A] EA [auth C] AA [auth B], BA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.185 (Depositor), 0.186 (DCC)
R-Value Work: 0.162 (Depositor)
R-Value Observed: 0.162 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.98	α = 90
b = 116.08	β = 119.755
c = 107.33	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-10-22
Changes: Structure summary