7RK3 | pdb_00007rk3

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

  • 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)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.220 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.159 (Depositor) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

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.

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

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase 1391Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30419
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ADP-ribosylation factor 68Homo sapiensMutation(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 
Entity Groups
UniProt GroupP62330
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.220 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.159 (Depositor) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.984α = 90
b = 76.046β = 90
c = 106.342γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXphasing
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK107868-04
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124165-01
National Institutes of Health/Office of the DirectorS10OD021527
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • 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