5NPQ

Human N-myristoyltransferase 1 (MNT1) with Myristoyl-CoA analogue X10 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.372 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Human N-myristoyltransferase 1 (MNT1) with Myristoyl-CoA analogue X10 bound.

Shen, M.Perez-Dorado, I.Fedoryshchak, R.Tate, E.W.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycylpeptide N-tetradecanoyltransferase 1
A, B
391Homo sapiensMutation(s): 0 
Gene Names: NMT1 (NMT)
EC: 2.3.1.97
Find proteins for P30419 (Homo sapiens)
Go to Gene View: NMT1
Go to UniProtKB:  P30419
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
94Q
Query on 94Q

Download SDF File 
Download CCD File 
A, B
~{S}-[2-[3-[[(2~{S})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 9-(3-but-3-ynyl-1,2-diazirin-3-yl)nonanethioate
Myristoyl-CoA analogue X10
C35 H56 N9 O17 P3 S
MSSDNISEPWMHOQ-CUJMRACVSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.372 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.972α = 90.00
b = 177.454β = 90.00
c = 58.244γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Cootmodel building
PDB_EXTRACTdata extraction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MMVUnited Kingdom--
Lee family scholarshipUnited Kingdom--

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-06
    Type: Data collection, Database references