5V0X

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001114


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001114

Mayclin, S.J.Abendroth, J.Lorimer, D.D.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferaseA, B, C405Plasmodium 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYA (Subject of Investigation/LOI)
Query on MYA

Download Ideal Coordinates CCD File 
D [auth A], N [auth B], V [auth C]TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-GLTUGWJXDB
 Ligand Interaction
8RD (Subject of Investigation/LOI)
Query on 8RD

Download Ideal Coordinates CCD File 
E [auth A], O [auth B], W [auth C]{4-[2-(5-fluoro-2-{3-[(methylamino)methyl][1,2,4]triazolo[4,3-a]pyridin-6-yl}phenoxy)ethyl]-1,5-dimethyl-1H-pyrazol-3-yl}(morpholin-4-yl)methanone
C26 H30 F N7 O3
NIWAAHIPMDGEGU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , 
AA [auth C],  BA [auth C],  CA [auth C],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  Y [auth C],  Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A], P [auth B], X [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.2α = 90
b = 118.01β = 90
c = 173.71γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release