8W8L

Crystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-38

PDB DOI: https://doi.org/10.2210/pdb8W8L/pdb

Classification: LIGASE
Organism(s): Pseudomonas aeruginosa 148
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-09-03 Released: 2024-09-04
Deposition Author(s): Luo, Z., Zhou, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.241
R-Value Work: 0.211

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure-Guided Fluorine Scanning Accelerates the Discovery of Potent and Selective Inhibitors Against Bacterial Prolyl-tRNA Synthetase

Luo, Z., Zhou, H.

To be published.

Macromolecule Content

Total Structure Weight: 130.51 kDa
Atom Count: 9,700
Modelled Residue Count: 1,135
Deposited Residue Count: 1,158
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline--tRNA ligase	A, B	579	Pseudomonas aeruginosa 148	Mutation(s): 0 Gene Names: proS EC: 6.1.1.15
UniProt
Find proteins for Q9I502 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I502 Go to UniProtKB: Q9I502
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I502
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W20 (Subject of Investigation/LOI) Query on W20 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain R [auth B] mmCIF format, chain C [auth A] mmCIF format, chain R [auth B]	C [auth A], R [auth B]	(2~{S})-~{N}-[5-(4-azanyl-8-fluoranyl-quinazolin-7-yl)-2-fluoranyl-phenyl]sulfonylpyrrolidine-2-carboxamide C₁₉ H₁₇ F₂ N₅ O₃ S CWXTYUZHOSSKNP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain R [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain S [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain S [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain S [auth B]	D [auth A], E [auth A], S [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain S [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] M [auth A] N [auth A] O [auth A] AA [auth B], BA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
MG Query on MG Download Ideal Coordinates CCD File 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] SDF format, chain L [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] 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] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], T [auth B], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions 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] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density 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] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B]