7QC1 | pdb_00007qc1

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436

PDB DOI: https://doi.org/10.2210/pdb7QC1/pdb

Classification: LIGASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-11-22 Released: 2021-12-08
Deposition Author(s): Johansson, C., Tye, M., Payne, N.C., Mazitschek, R., Oppermann, U.C.T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.233 (Depositor), 0.237 (DCC)
R-Value Work:
0.191 (Depositor), 0.196 (DCC)
R-Value Observed:
0.194 (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

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436

Johansson, C., Tye, M., Payne, N.C., Mazitschek, R., Oppermann, U.C.T.

To be published.

Macromolecule Content

Total Structure Weight: 178.86 kDa
Atom Count: 11,925
Modeled Residue Count: 1,455
Deposited Residue Count: 1,512
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline--tRNA ligase	A, B [auth D], C [auth I]	504	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
9XM (Subject of Investigation/LOI) Query on 9XM Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth D] SDF format, chain M [auth I] MOL2 format, chain D [auth A] MOL2 format, chain J [auth D] MOL2 format, chain M [auth I] mmCIF format, chain D [auth A] mmCIF format, chain J [auth D] mmCIF format, chain M [auth I]	D [auth A], J [auth D], M [auth I]	[(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate C₃₆ H₃₈ Br Cl N₁₀ O₈ S LACGGYFSTYXEOM-IHLOFXLRSA-N		Interactions Focus chain D [auth A] Focus chain J [auth D] Focus chain M [auth I] Interactions & Density Focus chain D [auth A] Focus chain J [auth D] Focus chain M [auth I]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth I] SDF format, chain O [auth I] SDF format, chain N [auth I] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth I] MOL2 format, chain O [auth I] MOL2 format, chain N [auth I] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth I] mmCIF format, chain O [auth I] mmCIF format, chain N [auth I] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [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], K [auth D], L [auth D], N [auth I], O [auth I], P [auth I]	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 K [auth D] Focus chain L [auth D] Focus chain N [auth I] Focus chain O [auth I] Focus chain P [auth I] 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 K [auth D] Focus chain L [auth D] Focus chain N [auth I] Focus chain O [auth I] Focus chain P [auth I]