7Q2M | pdb_00007q2m

Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with but-3-yn-2-amine hydrochloride

PDB DOI: https://doi.org/10.2210/pdb7Q2M/pdb

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

Deposited: 2021-10-25 Released: 2022-11-23
Deposition Author(s): Duclovel, C., Gelin, M., Krimm, I., Cerdan, R., Guichou, J.F.
Funding Organization(s): Montpellier University of Excellence (MUSE)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.234 (Depositor), 0.230 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design of PfCCT inhibitors.

Duclovel, C., Gelin, M., Wein, S., Wengelnik, K., Krimm, I., Guichou, J.F., Cerdan, R.

To be published.

Macromolecule Content

Total Structure Weight: 20.95 kDa
Atom Count: 1,105
Modeled Residue Count: 130
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinephosphate cytidylyltransferase	A	180	Plasmodium falciparum	Mutation(s): 0 Gene Names: ctP, MAL13P1.86 EC: 2.7.7.15
UniProt
Find proteins for Q8IEE9 (Plasmodium falciparum (isolate 3D7)) Explore Q8IEE9 Go to UniProtKB: Q8IEE9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IEE9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8PN (Subject of Investigation/LOI) Query on 8PN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	(2S)-but-3-yn-2-amine C₄ H₇ N ZZRMYOZQUCUWFT-BYPYZUCNSA-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: 2.08 Å
R-Value Free: 0.234 (Depositor), 0.230 (DCC)
R-Value Work: 0.209 (Depositor), 0.210 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.3	α = 90
b = 68.991	β = 90
c = 117.534	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Montpellier University of Excellence (MUSE)	France	--

Revision History (Full details and data files)

Version 1.0: 2022-11-23
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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.