5V0W

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001088


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.184 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.147 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MYAClick on this verticalbar to view detailsBest fitted KFKClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structure of Plasmodium vivax N-myristoyltransferase with inhibitor IMP-1088: exploring an NMT inhibitor for antimalarial therapy

Mendez, A.Bolling, C.Taylor, S.Makumire, S.Staker, B.Reers, A.Hammerson, B.Mayclin, S.J.Abendroth, J.Lorimer, D.D.Edwards, T.E.Tate, E.W.Subramanian, S.Bell, A.S.Myler, P.J.Asojo, O.A.Chakafana, G.

(2025) Acta Crystallogr F Struct Biol Commun 81: 1-10


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase
A, B, C
405Plasmodium vivaxMutation(s): 0 
Gene Names: PVC01_130042700PVP01_1336100
EC: 2.3.1.97
UniProt
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I))
Explore A5K1A2 
Go to UniProtKB:  A5K1A2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K1A2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYA
Query on MYA

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B],
S [auth C]
TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-QSGBVPJFSA-N
KFK
Query on KFK

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
T [auth C]
1-[5-[3,4-bis(fluoranyl)-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-1-methyl-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine
C25 H29 F2 N5 O
SOXNKJCQBRQUMS-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A],
Q [auth B],
R [auth B],
X [auth C],
Y [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.184 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.32α = 90
b = 119.13β = 90
c = 176.61γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MYAClick on this verticalbar to view detailsBest fitted KFKClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2025-01-15
    Changes: Database references, Structure summary