8U2S

Crystal Structure of Acetyl-coenzyme A synthetase from Leishmania infantum (Ethyl AMP bound, P21 form)

PDB DOI: https://doi.org/10.2210/pdb8U2S/pdb

Classification: LIGASE
Organism(s): Leishmania infantum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-06 Released: 2023-09-13
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: 2.52 Å
R-Value Free: 0.219
R-Value Work: 0.186
R-Value Observed: 0.188

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-coenzyme A synthetase from Leishmania infantum (Ethyl AMP bound, P21 form)

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

To be published.

Macromolecule Content

Total Structure Weight: 161.24 kDa
Atom Count: 10,295
Modelled Residue Count: 1,301
Deposited Residue Count: 1,426
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	713	Leishmania infantum	Mutation(s): 0 Gene Names: LINJ_23_0580
UniProt
Find proteins for A4I093 (Leishmania infantum) Explore A4I093 Go to UniProtKB: A4I093
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4I093
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WTA (Subject of Investigation/LOI) Query on WTA Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain N [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain N [auth A]	BA [auth B], N [auth A]	5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine C₁₂ H₁₈ N₅ O₇ P MXYRBUKSSSUFQO-WOUKDFQISA-N		Interactions Focus chain BA [auth B] Focus chain N [auth A] Interactions & Density Focus chain BA [auth B] Focus chain N [auth A]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	C [auth A] D [auth A] E [auth A] O [auth B] P [auth B] C [auth A], D [auth A], E [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain F [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	F [auth A], S [auth B], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain F [auth A] Focus chain S [auth B] Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] G [auth A] H [auth A] I [auth A] J [auth A] AA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] 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 G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] 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: 2.52 Å
R-Value Free: 0.219
R-Value Work: 0.186
R-Value Observed: 0.188
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M38U2S

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.206	α = 90
b = 61.815	β = 92.98
c = 134.81	γ = 90

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: 2023-09-13

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