7RK3 | pdb_00007rk3

Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A

• PDB DOI: https://doi.org/10.2210/pdb7RK3/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), unidentified
• Mutation(s): No 


• Deposited: 2021-07-21 Released: 2022-07-27 
• Deposition Author(s): Fenwick, M.K., Lin, H.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director, Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: other

Literature

Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A

Fenwick, M.K., Lin, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 47.13 kDa 
• Atom Count: 3,513 
• Modeled Residue Count: 360 
• Deposited Residue Count: 399 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase 1	A	391	Homo sapiens	Mutation(s): 0  Gene Names: NMT1, NMT 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor 6	B	8	Homo sapiens	Mutation(s): 0  Gene Names: ARF6 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P62330 (Homo sapiens) Explore P62330  Go to UniProtKB:  P62330
PHAROS:  P62330 GTEx:  ENSG00000165527

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4PS (Subject of Investigation/LOI)	C [auth A]	4'-diphospho pantetheine C11 H24 N2 O10 P2 S UQURMDBHCKDEJS-VIFPVBQESA-N
MYR (Subject of Investigation/LOI)	D [auth B]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
6NA (Subject of Investigation/LOI)	E [auth B]	HEXANOIC ACID C6 H12 O2 FUZZWVXGSFPDMH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.984	α = 90
b = 76.046	β = 90
c = 106.342	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	phasing
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Fenwick, M.K., Lin, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK107868-04
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM124165-01
National Institutes of Health/Office of the Director		S10OD021527
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary