6HY1

Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine after catalysis in crystal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine after catalysis in crystal

Sprenger, J.Coertzen, D.Persson, L.Carey, J.Birkholtz, L.M.Louw, B.I.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermidine synthase
A, B, C
281Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1129000
EC: 2.5.1.16
UniProt
Find proteins for Q8II73 (Plasmodium falciparum (isolate 3D7))
Explore Q8II73 
Go to UniProtKB:  Q8II73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8II73
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MTA
Query on MTA

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
O [auth C]
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
1PG
Query on 1PG

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
GXQ
Query on GXQ

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine
C12 H28 N4
PYBOSIQOXDJMFB-HAQNSBGRSA-N
JFQ
Query on JFQ

Download Ideal Coordinates CCD File 
N [auth C]trans-N-(3-aminopropyl)cyclohexane-1,4-diamine
C9 H21 N3
QIMPCSMJRMPRJC-KYZUINATSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
L [auth B]
M [auth B]
P [auth C]
G [auth A],
J [auth B],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
R [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MTA BindingDB:  6HY1 IC50: 1.59e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.87α = 90
b = 135β = 95.95
c = 48.57γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references