7F9U | pdb_00007f9u

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor T35 and Halofuginone

PDB DOI: https://doi.org/10.2210/pdb7F9U/pdb

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

Deposited: 2021-07-04 Released: 2022-07-06
Deposition Author(s): Manickam, Y., Malhotra, N., Sharma, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.224 (Depositor), 0.220 (DCC)
R-Value Work:
0.164 (Depositor), 0.160 (DCC)
R-Value Observed:
0.166 (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

TgPRS with double inhibitors

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

To be published.

Macromolecule Content

Total Structure Weight: 236 kDa
Atom Count: 15,950
Modeled Residue Count: 1,931
Deposited Residue Count: 2,000
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl-tRNA synthetase (ProRS)	A, B, C, D	500	Toxoplasma gondii	Mutation(s): 0 Gene Names: TGRH88_057780 EC: 6.1.1.15
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 F [auth A] SDF format, chain N [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	F [auth A], N [auth B], U [auth C], Y [auth D]	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 F [auth A] Focus chain N [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain N [auth B] Focus chain U [auth C] Focus chain Y [auth D]
HFG Query on HFG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	E [auth A], M [auth B], T [auth C], X [auth D]	7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one C₁₆ H₁₇ Br Cl N₃ O₃ LVASCWIMLIKXLA-CABCVRRESA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain X [auth D]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain Z [auth D] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Z [auth D]	G [auth A], O [auth B], Z [auth D]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain O [auth B] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain O [auth B] Focus chain Z [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B]	H [auth A], I [auth A], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	J [auth A] K [auth A] L [auth A] Q [auth B] R [auth B] J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], V [auth C], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C]