6OMK | pdb_00006omk

Crystal structure of a glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase, NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA

• PDB DOI: https://doi.org/10.2210/pdb6OMK/pdb

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


• Deposited: 2019-04-18 Released: 2019-05-01 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase, NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA

Edwards, T.E., Horanyi, P.S., Bertolin, B.A., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.26 kDa 
• Atom Count: 3,648 
• Modeled Residue Count: 417 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase	A	424	Leishmania major	Mutation(s): 0  Gene Names: NMT EC: 2.3.1.97
UniProt
Find proteins for Q9GPZ4 (Leishmania major) Explore Q9GPZ4  Go to UniProtKB:  Q9GPZ4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA	B [auth A]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.25	α = 90
b = 89.17	β = 90
c = 90.36	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-01 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-05-01
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description