7V8J | pdb_00007v8j

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with the reaction intermediates proline-adenylate (Pro-AMP) and pyrophosphate

PDB DOI: https://doi.org/10.2210/pdb7V8J/pdb

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

Deposited: 2021-08-23 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: 2.52 Å
R-Value Free:
0.226 (Depositor), 0.231 (DCC)
R-Value Work:
0.169 (Depositor), 0.182 (DCC)
R-Value Observed:
0.172 (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

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with the reaction intermediates proline-adenylate (Pro-AMP) and pyrophosphate

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

To be published.

Macromolecule Content

Total Structure Weight: 116.86 kDa
Atom Count: 7,932
Modeled Residue Count: 954
Deposited Residue Count: 1,000
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl-tRNA synthetase	A, B	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7J6JUK2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PR8 (Subject of Investigation/LOI) Query on PR8 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]	5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine C₁₅ H₂₁ N₆ O₈ P KQFKHTAASHMYDJ-TWBCTODHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PPV Query on PPV Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PRO Query on PRO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]