2QOR | pdb_00002qor

Crystal structure of Plasmodium vivax guanylate kinase

• PDB DOI: https://doi.org/10.2210/pdb2QOR/pdb

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


• Deposited: 2007-07-20 Released: 2007-08-07 
• Deposition Author(s): Merritt, E.A., Le Trong, I., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.227 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Plasmodium vivax guanylate kinase.

Le Trong, I., Merritt, E.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.49 kDa 
• Atom Count: 1,697 
• Modeled Residue Count: 196 
• Deposited Residue Count: 204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate kinase	A	204	Plasmodium vivax	Mutation(s): 0  Gene Names: Pv099895, PVX_099895 EC: 2.7.4.8
UniProt
Find proteins for A5K709 (Plasmodium vivax (strain Salvador I)) Explore A5K709  Go to UniProtKB:  A5K709

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	B [auth A]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
POP	C [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.227 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.535	α = 90
b = 43.535	β = 90
c = 342.8	γ = 120

Software Package:

Software Name	Purpose
TRUNCATE	data reduction
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Merritt, E.A., Le Trong, I., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary