1RXT | pdb_00001rxt

Crystal structure of human myristoyl-CoA:protein N-myristoyltransferase.

• PDB DOI: https://doi.org/10.2210/pdb1RXT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-18 Released: 2005-04-12 
• Deposition Author(s): Yang, J., Wang, Y., Frey, G., Abeles, R.H., Petsko, G.A., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.391 (Depositor), 0.407 (DCC) 
• R-Value Work: 
  0.283 (Depositor), 0.337 (DCC) 

Literature

Crystal structure of human myristoyl-CoA:protein N-myristoyltransferase

Yang, J., Wang, Y., Frey, G., Abeles, R.H., Petsko, G.A., Ringe, D.

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 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.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 227.98 kDa 
• Atom Count: 10,420 
• Modeled Residue Count: 1,335 
• Deposited Residue Count: 1,984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase 1	A, B, C, D	496	Homo sapiens	Mutation(s): 0  EC: 2.3.1.97 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30419 (Homo sapiens) Explore P30419  Go to UniProtKB:  P30419
PHAROS:  P30419 GTEx:  ENSG00000136448

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth B], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO	H [auth C]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.391 (Depositor), 0.407 (DCC) 
• R-Value Work:  0.283 (Depositor), 0.337 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.626	α = 90
b = 116.425	β = 90.13
c = 90.361	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-12 
Deposition Author(s): Yang, J., Wang, Y., Frey, G., Abeles, R.H., Petsko, G.A., Ringe, D.

Revision History  

• Version 1.0: 2005-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations