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), 0.193 (DCC)
R-Value Work:
0.155 (Depositor), 0.162 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.193 (DCC)
R-Value Work: 0.155 (Depositor), 0.162 (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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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

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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.