3EZ3

Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound

Wernimont, A.K.Lew, J.Zhao, Y.Kozieradzki, I.Cossar, D.Schapira, M.Bochkarev, A.Arrowsmith, C.H.Bountra, C.Weigelt, J.Edwards, A.M.Hui, R.Artz, J.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthase, putative
A, B, C, D
396Plasmodium vivaxMutation(s): 0 
Gene Names: PVX_092040
UniProt
Find proteins for A5K4U6 (Plasmodium vivax (strain Salvador I))
Explore A5K4U6 
Go to UniProtKB:  A5K4U6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K4U6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZOL
Query on ZOL

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
S [auth C],
X [auth D]
ZOLEDRONIC ACID
C5 H10 N2 O7 P2
XRASPMIURGNCCH-UHFFFAOYSA-N
IPE
Query on IPE

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
T [auth C],
Y [auth D]
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
C5 H12 O7 P2
NUHSROFQTUXZQQ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth D],
K [auth A],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
G [auth A]
H [auth A]
I [auth A]
AA [auth D],
BA [auth D],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
U [auth C],
V [auth C],
W [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.266α = 90
b = 109.696β = 90
c = 139.529γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-12-27
    Changes: Advisory, Data collection, Database references, Derived calculations