7F96 | pdb_00007f96

Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L95

PDB DOI: https://doi.org/10.2210/pdb7F96/pdb

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

Deposited: 2021-07-04 Released: 2023-01-04
Deposition Author(s): Mishra, S., Malhotra, N., Yogavel, M., Sharma, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free:
0.191 (Depositor), 0.190 (DCC)
R-Value Work:
0.155 (Depositor), 0.160 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

ATP mimetics targeting prolyl-tRNA synthetases as a new avenue for antimalarial drug development

Mishra, S., Malhotra, N., Laleu, B., Chakraborti, S., Yogavel, M., Sharma, A.

(2024) iScience 27

DOI: https://doi.org/10.1016/j.isci.2024.110049

Macromolecule Content

Total Structure Weight: 58.29 kDa
Atom Count: 4,057
Modeled Residue Count: 487
Deposited Residue Count: 497
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline--tRNA ligase	A	497	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: proRS, PFL0670c EC: 6.1.1.15
UniProt
Find proteins for Q8I5R7 (Plasmodium falciparum (isolate 3D7)) Explore Q8I5R7 Go to UniProtKB: Q8I5R7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8I5R7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JE6 (Subject of Investigation/LOI) Query on JE6 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]	~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide C₂₂ H₂₂ N₄ O₂ FLWLQSFDWRRFDA-JOCHJYFZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PRO Query on PRO 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]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.191 (Depositor), 0.190 (DCC)
R-Value Work: 0.155 (Depositor), 0.160 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.61	α = 90
b = 103.61	β = 90
c = 128.04	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-01-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-01-04
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection
Version 1.2: 2024-07-31
Changes: Database references, Structure summary

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.