4QBJ | pdb_00004qbj

Crystal structure of N-myristoyl transferase from Aspergillus fumigatus complexed with a synthetic inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4QBJ/pdb

• Classification: Transferase/Transferase inhibitor
• Organism(s): Aspergillus fumigatus Af293
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-08 Released: 2015-04-01 
• Deposition Author(s): Suzuki, M., Shimada, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.217 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Structure of N-myristoyltransferase from Aspergillus fumigatus

Shimada, T., Suzuki, M., Katakura, S.

(2015) Acta Crystallogr D Biol Crystallogr 71: 754-761

• PubMed: 25849386 
• DOI: https://doi.org/10.1107/S1399004715000401
• Primary Citation Related Structures: 
  4QBJ


• PubMed Abstract: 
  

  N-Myristoyltransferase (NMT) is an enzyme which translocates the 14-carbon saturated fatty acid myristate from myristoyl-CoA to the N-terminal glycine of substrate peptides. This myristoylation process is involved in protein modification in various eukaryotes, including animals and fungi. Furthermore, this enzyme has been shown to be essential to the growth of various species, such as Saccharomyces cerevisiae, which indicates that NMT is an attractive target for the development of a novel antifungal drug. In this study, the crystal structure of a ternary complex of NMT from Aspergillus fumigatus with S-(2-oxo)pentadecyl-CoA, a myristoyl-CoA analogue cofactor, and a synthetic inhibitor is reported at a resolution of 2.1 Å. The results advance the understanding of the specificity of NMT inhibitors and provide valuable information for structure-based drug design.

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Organizational Affiliation: 
• Drug Discovery and Biomedical Technology Unit, Daiichi Sankyo RD Novare Co. Ltd, 1-16-13 Kita-kasai, Edogawa-ku, Tokyo 134-8630, Japan.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 47.49 kDa 
• Atom Count: 3,401 
• Modeled Residue Count: 396 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase	A	396	Aspergillus fumigatus Af293	Mutation(s): 0  Gene Names: nmt1 EC: 2.3.1.97
UniProt
Find proteins for Q9UVX3 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q9UVX3  Go to UniProtKB:  Q9UVX3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHM	E [auth A]	S-(2-OXO)PENTADECYLCOA C36 H64 N7 O17 P3 S JKWHUJMJVNMKEF-SXKLBCNJSA-N
2XQ	F [auth A]	3-[[3-methyl-2-[[2,3,4-tris(fluoranyl)phenoxy]methyl]-1-benzofuran-4-yl]oxy]-N-(pyridin-3-ylmethyl)propan-1-amine C25 H23 F3 N2 O3 FKIAZUIISXQFHC-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.217 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.792	α = 90
b = 77.074	β = 90
c = 113.237	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Suzuki, M., Shimada, T.

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Database references
• Version 1.2: 2015-04-22
  Changes: Database references
• Version 1.3: 2016-12-21
  Changes: Structure summary
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description