9HSG | pdb_00009hsg

Crystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with CDP-Choline

PDB DOI: https://doi.org/10.2210/pdb9HSG/pdb

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

Deposited: 2024-12-19 Released: 2025-02-05
Deposition Author(s): Audebert, S., Gelin, M., Guichou, J.-F.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.243 (Depositor), 0.241 (DCC)
R-Value Work:
0.225 (Depositor), 0.224 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with CDP-Choline

Audebert, S., Guichou, J.-F., Gelin, M.

To be published.

Macromolecule Content

Total Structure Weight: 21.14 kDa
Atom Count: 1,148
Modelled Residue Count: 140
Deposited Residue Count: 179
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-phosphate cytidylyltransferase	A	179	Plasmodium falciparum	Mutation(s): 0 Gene Names: PF3D7_1316600 EC: 2.7.7.15
UniProt
Find proteins for P49587 (Plasmodium falciparum (isolate K1 / Thailand)) Explore P49587 Go to UniProtKB: P49587
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49587
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDC (Subject of Investigation/LOI) Query on CDC 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]	[2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM C₁₄ H₂₆ N₄ O₁₁ P₂ RZZPDXZPRHQOCG-OJAKKHQRSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.243 (Depositor), 0.241 (DCC)
R-Value Work: 0.225 (Depositor), 0.224 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.267	α = 90
b = 70.805	β = 90
c = 118.166	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-20-CE44-0012

Revision History (Full details and data files)

Version 1.0: 2025-02-05
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.