5NPQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase 1A, B391Homo sapiensMutation(s): 0 
Gene Names: NMT1NMT
EC: 2.3.1.97
UniProt & NIH Common Fund Data Resources
Find proteins for P30419 (Homo sapiens)
Explore P30419 
Go to UniProtKB:  P30419
PHAROS:  P30419
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
94Q (Subject of Investigation/LOI)
Query on 94Q

Download Ideal Coordinates CCD File 
E [auth A], I [auth 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
C35 H56 N9 O17 P3 S
MSSDNISEPWMHOQ-CUJMRACVSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], G [auth B], H [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A], J [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.972α = 90
b = 177.454β = 90
c = 58.244γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

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