7QC2 | pdb_00007qc2

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT334 and L-Proline

• PDB DOI: https://doi.org/10.2210/pdb7QC2/pdb

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


• Deposited: 2021-11-22 Released: 2022-05-04 
• Deposition Author(s): Johansson, C., Tye, M., Payne, N.C., Mazitschek, R., Oppermann, U.C.T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT334 and L-Proline

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.31 kDa 
• Atom Count: 3,957 
• Modeled Residue Count: 492 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline--tRNA ligase	A	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AJT (Subject of Investigation/LOI)	C [auth A]	~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-[[4-[[(2~{S})-pyrrolidin-2-yl]carbonylamino]piperidin-1-yl]carbonylamino]pyrazine-2-carboxamide C25 H31 N7 O3 ZDFMGZGZVIOGCH-FQEVSTJZSA-N
PRO	B [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.5	α = 90
b = 103.5	β = 90
c = 127.51	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): Johansson, C., Tye, M., Payne, N.C., Mazitschek, R., Oppermann, U.C.T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description