7VC5

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor T35 and Febrifugine (FF) at 1.61 A resolution

PDB DOI: https://doi.org/10.2210/pdb7VC5/pdb

Classification: LIGASE/LIGASE INHIBITOR
Organism(s): Toxoplasma gondii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-09-01 Released: 2022-09-07
Deposition Author(s): Manickam, Y., Malhotra, N., Sharma, A.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.196
R-Value Work: 0.165
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

TgPRS with double inhibitors

Malhotra, N., Manickam, Y., Sharma, A.

To be published.

Macromolecule Content

Total Structure Weight: 59.43 kDa
Atom Count: 4,319
Modelled Residue Count: 485
Deposited Residue Count: 500
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl-tRNA synthetase (ProRS)	A	500	Toxoplasma gondii	Mutation(s): 0 Gene Names: TGRH88_057780
UniProt
Find proteins for A0A7J6JUK2 (Toxoplasma gondii) Explore A0A7J6JUK2 Go to UniProtKB: A0A7J6JUK2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7J6JUK2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1TI (Subject of Investigation/LOI) Query on 1TI Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	4-[(3S)-3-cyano-3-(1-methylcyclopropyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide C₂₇ H₂₇ F N₆ O₂ PFICVJYRZDMEIX-MHZLTWQESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
9SF Query on 9SF Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one C₁₆ H₁₉ N₃ O₃ FWVHWDSCPKXMDB-CABCVRRESA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]