5EZR | pdb_00005ezr

Crystal Structure of PVX_084705 bound to compound

• PDB DOI: https://doi.org/10.2210/pdb5EZR/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium vivax Sal-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-26 Released: 2017-05-10 
• Deposition Author(s): El Bakkouri, M., Amani, M., Walker, J.R., Osborne, S., Large, J.M., Birchall, K., Bouloc, N., Smiljanic-Hurley, E., Wheldon, M., Harding, D.J., Merritt, A.T., Ansell, K.H., Coombs, P.J., Kettleborough, C.A., Stewart, B.L., Bowyer, P.W., Gutteridge, W.E., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Baker, D.A., Hui, R., Loppnau, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.266 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.225 (Depositor) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of PVX_084705 bound to compound

El Bakkouri, M., Amani, M., Walker, J.R., Osborne, S., Large, J.M., Birchall, K., Bouloc, N., Smiljanic-Hurley, E., Wheldon, M., Harding, D.J., Merritt, A.T., Ansell, K.H., Coombs, P.J., Kettleborough, C.A., Stewart, B.L., Bowyer, P.W., Gutteridge, W.E., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Baker, D.A., Hui, R., Loppnau, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.23 kDa 
• Atom Count: 6,308 
• Modeled Residue Count: 803 
• Deposited Residue Count: 846 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-dependent protein kinase, putative	A	846	Plasmodium vivax Sal-1	Mutation(s): 0  Gene Names: PVX_084705 EC: 2.7.11.12
UniProt
Find proteins for A5K0N4 (Plasmodium vivax (strain Salvador I)) Explore A5K0N4  Go to UniProtKB:  A5K0N4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4ZS	B [auth A]	N-[5-(3-{2-[(cyclopropylmethyl)amino]pyrimidin-4-yl}-7-[(dimethylamino)methyl]-6-methylimidazo[1,2-a]pyridin-2-yl)-2-fluorophenyl]methanesulfonamide C26 H30 F N7 O2 S LDISLUXUWYPJIZ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.266 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.225 (Depositor) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.103	α = 90
b = 117.967	β = 95.17
c = 68.162	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): El Bakkouri, M., Amani, M., Walker, J.R., Osborne, S., Large, J.M., Birchall, K., Bouloc, N., Smiljanic-Hurley, E., Wheldon, M., Harding, D.J., Merritt, A.T., Ansell, K.H., Coombs, P.J., Kettleborough, C.A., Stewart, B.L., Bowyer, P.W., Gutteridge, W.E., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Baker, D.A., Hui, R., Loppnau, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description