Macromolecule Content

Total Structure Weight: 46.15 kDa
Atom Count: 3,277
Modelled Residue Count: 359
Deposited Residue Count: 382
Unique protein chains: 1

6YXS

Crystal structure of the apo form of choline kinase from Plasmodium falciparum

PDB DOI: 10.2210/pdb6YXS/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-05-03 Released: 2020-08-05
Deposition Author(s): Torretta, A., Parisini, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.238
R-Value Work: 0.206
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of the Apo and the ADP-Bound Form of Choline Kinase from Plasmodium falciparum

Torretta, A., Lopez-Cara, L.C., Parisini, E.

(2020) Crystals (Basel)

DOI: 10.3390/cryst10070613

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline kinase	A	382	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF3D7_1401800 EC: 2.7.1.32
UniProt
Find proteins for Q8IM71 (Plasmodium falciparum (isolate 3D7)) Explore Q8IM71 Go to UniProtKB: Q8IM71
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IM71
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.238
R-Value Work: 0.206
R-Value Observed: 0.208
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.41	α = 90
b = 68.82	β = 90
c = 104.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.