4C68

Plasmodium vivax N-myristoyltransferase in complex with a peptidomimetic inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4C68/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-17 Released: 2014-09-24 
• Deposition Author(s): Olaleye, T.O., Brannigan, J.A., Goncalves, V., Roberts, S.M., Leatherbarrow, R.J., Wilkinson, A.J., Tate, E.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.260 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Literature

Peptidomimetic Inhibitors of N-Myristoyltransferase from Human Malaria and Leishmaniasis Parasites.

Olaleye, T.O., Brannigan, J.A., Roberts, S.M., Leatherbarrow, R.J., Wilkinson, A.J., Tate, E.W.

(2014) Org Biomol Chem 12: 8132

• PubMed: 25230674 
• DOI: https://doi.org/10.1039/c4ob01669f
• Primary Citation of Related Structures:  
  4C68, 4C7H, 4C7I


• PubMed Abstract: 
  

  N-Myristoyltransferase (NMT) has been shown to be essential in Leishmania and subsequently validated as a drug target in Plasmodium. Herein, we discuss the use of antifungal NMT inhibitors as a basis for inhibitor development resulting in the first sub-micromolar peptidomimetic inhibitors of Plasmodium and Leishmania NMTs. High-resolution structures of these inhibitors with Plasmodium and Leishmania NMTs permit a comparative analysis of binding modes, and provide the first crystal structure evidence for a ternary NMT-Coenzyme A/myristoylated peptide product complex.

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Organizational Affiliation: 

Department of Chemistry, Imperial College London, London, SW7 2AZ, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 139.62 kDa 
• Atom Count: 11,510 
• Modelled Residue Count: 1,138 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE	A, B, C	384	Plasmodium vivax	Mutation(s): 0  EC: 2.3.1.97
UniProt
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I)) Explore A5K1A2  Go to UniProtKB:  A5K1A2

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHW	G [auth A], N [auth B], S [auth C]	2-oxopentadecyl-CoA C36 H64 N7 O17 P3 S JKWHUJMJVNMKEF-UOCZADIYSA-J
EN5	F [auth A], M [auth B]	N-(10-aminodecanoyl)-L-seryl-N-(2-cyclohexylethyl)-L-lysinamide C27 H53 N5 O4 OVRFOVZVAWIPDE-ZEQRLZLVSA-N
SO4	J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	E [auth A], K [auth A], L [auth B], Q [auth B], R [auth C]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	H [auth A], O [auth B], T [auth C], U [auth C], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	I [auth A], P [auth B], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.260 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.33	α = 90
b = 121.43	β = 90
c = 178.74	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Olaleye, T.O., Brannigan, J.A., Goncalves, V., Roberts, S.M., Leatherbarrow, R.J., Wilkinson, A.J., Tate, E.W.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 1.2: 2014-10-08
  Changes: Database references
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other