3FI8

Crystal structure of choline kinase from Plasmodium Falciparum, PF14_0020

PDB DOI: https://doi.org/10.2210/pdb3FI8/pdb

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

Deposited: 2008-12-11 Released: 2009-02-10
Deposition Author(s): Wernimont, A.K., Pizarro, J.C., Artz, J.D., Amaya, M.F., Xiao, T., Lew, J., Wasney, G., Senesterra, G., Kozieradzki, I., Cossar, D., Vedadi, M., Schapira, M., Bochkarev, A., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hui, R., Hills, T., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.265 (Depositor), 0.270 (DCC)
R-Value Work:
0.197 (Depositor), 0.190 (DCC)
R-Value Observed:
0.200 (Depositor)

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 choline kinase from Plasmodium Falciparum, PF14_0020

Wernimont, A.K., Pizarro, J.C., Artz, J.D., Amaya, M.F., Xiao, T., Lew, J., Wasney, G., Senesterra, G., Kozieradzki, I., Cossar, D., Vedadi, M., Schapira, M., Bochkarev, A., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hui, R., Hills, T.

To be published.

Macromolecule Content

Total Structure Weight: 43.79 kDa
Atom Count: 2,964
Modelled Residue Count: 339
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline kinase	A	362	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF14_0020 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
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
OPE Query on OPE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER C₂ H₈ N O₄ P SUHOOTKUPISOBE-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.265 (Depositor), 0.270 (DCC)
R-Value Work: 0.197 (Depositor), 0.190 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.38	α = 90
b = 64.556	β = 90
c = 91.557	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-02-10

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-02-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations