5EGL | pdb_00005egl

The structural and biochemical characterization of acyl-coa hydrolase from Staphylococcus aureus in complex with Butyryl Coenzyme A, Coenzyme A, and Coenzyme A disulfide

• PDB DOI: https://doi.org/10.2210/pdb5EGL/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-27 Released: 2016-11-09 
• Deposition Author(s): Khandokar, Y.B., Srivastava, P.S., Forwood, J.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.246 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

The structural and biochemical characterization of acyl-coa hydrolase from Staphylococcus aureus

Khandokar, Y.B., Srivastava, P.S., Forwood, J.K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.12 kDa 
• Atom Count: 4,312 
• Modeled Residue Count: 492 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl CoA Hydrolase	A, B, C	176	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: SAV1878
UniProt
Find proteins for A0A0H3K033 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3K033  Go to UniProtKB:  A0A0H3K033

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5NG	F [auth C]	[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate C42 H70 N14 O32 P6 S2 YAISMNQCMHVVLO-BJLFRJKCSA-N
BCO	D [auth A]	Butyryl Coenzyme A C25 H42 N7 O17 P3 S CRFNGMNYKDXRTN-CITAKDKDSA-N
COA	E [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.246 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.26	α = 90
b = 142.26	β = 90
c = 163.892	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Khandokar, Y.B., Srivastava, P.S., Forwood, J.K.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description