3TLX | pdb_00003tlx

Crystal Structure of PF10_0086, adenylate kinase from plasmodium falciparum

• PDB DOI: https://doi.org/10.2210/pdb3TLX/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum
• Mutation(s): No 


• Deposited: 2011-08-30 Released: 2011-10-26 
• Deposition Author(s): Wernimont, A.K., Loppnau, P., Crombet, L., Weadge, J., Perieteanu, A., Edwards, A.M., Arrowsmith, C.H., Park, H., Bountra, C., Hui, R., Amani, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.260 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal Structure of PF10_0086, adenylate kinase from plasmodium falciparum

Wernimont, A.K., Loppnau, P., Crombet, L., Weadge, J., Perieteanu, A., Edwards, A.M., Arrowsmith, C.H., Park, H., Bountra, C., Hui, R., Amani, M.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 113.03 kDa 
• Atom Count: 5,817 
• Modeled Residue Count: 812 
• Deposited Residue Count: 972 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase 2	A, B, C, D	243	Plasmodium falciparum	Mutation(s): 0  EC: 2.7.4.3
UniProt
Find proteins for Q8IJV6 (Plasmodium falciparum (isolate 3D7)) Explore Q8IJV6  Go to UniProtKB:  Q8IJV6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	K [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP	H [auth A], I [auth B], J [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP	G [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.260 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.395	α = 90
b = 76.663	β = 100.78
c = 93.768	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-26 
Deposition Author(s): Wernimont, A.K., Loppnau, P., Crombet, L., Weadge, J., Perieteanu, A., Edwards, A.M., Arrowsmith, C.H., Park, H., Bountra, C., Hui, R., Amani, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-10-26
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Structure summary
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations