9HSX | pdb_00009hsx

Crystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 2-aminopyridine

PDB DOI: https://doi.org/10.2210/pdb9HSX/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: 2.23 Å
R-Value Free:
0.274 (Depositor), 0.278 (DCC)
R-Value Work:
0.211 (Depositor), 0.212 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 2-aminopyridine

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

To be published.

Macromolecule Content

Total Structure Weight: 20.84 kDa
Atom Count: 1,100
Modeled Residue Count: 130
Deposited Residue Count: 179
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49587
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HVK (Subject of Investigation/LOI) Query on HVK Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	pyridin-2-amine C₅ H₆ N₂ ICSNLGPSRYBMBD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.274 (Depositor), 0.278 (DCC)
R-Value Work: 0.211 (Depositor), 0.212 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.354	α = 90
b = 70.945	β = 90
c = 119.638	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.