6TW8 | pdb_00006tw8

Leishmania major N-myristoyltransferase in complex with indazole inhibitor IMP-917

• PDB DOI: https://doi.org/10.2210/pdb6TW8/pdb

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


• Deposited: 2020-01-12 Released: 2021-07-21 
• Deposition Author(s): Brannigan, J.A.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 

Literature

Leishmania major N-myristoyltransferase in complex with indazole inhibitor IMP-917

Brannigan, J.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 99.24 kDa 
• Atom Count: 7,792 
• Modeled Residue Count: 822 
• Deposited Residue Count: 836 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase	A [auth AAA], B [auth CCC]	418	Leishmania major	Mutation(s): 0  Gene Names: NMT, LMJF_32_0080 EC: 2.3.1.97
UniProt
Find proteins for Q4Q5S8 (Leishmania major) Explore Q4Q5S8  Go to UniProtKB:  Q4Q5S8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA	C [auth AAA], F [auth CCC]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N
9M2 (Subject of Investigation/LOI)	D [auth AAA], G [auth CCC]	1-[5-[4-fluoranyl-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-2~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine C24 H28 F N5 O CGEINWMYWNHNPM-UHFFFAOYSA-N
MG	E [auth AAA], H [auth CCC]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.02	α = 90
b = 89.82	β = 104.27
c = 97.18	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Brannigan, J.A.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references, Derived calculations