7F97

Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L97


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

ATP mimetics targeting prolyl-tRNA synthetases as a new avenue for antimalarial drug development

Mishra, S.Malhotra, N.Laleu, B.Chakraborti, S.Yogavel, M.Sharma, A.

(2024) iScience 27


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proline--tRNA ligase
A, B, C, D
497Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: proRSPFL0670c
EC: 6.1.1.15
UniProt
Find proteins for Q8I5R7 (Plasmodium falciparum (isolate 3D7))
Explore Q8I5R7 
Go to UniProtKB:  Q8I5R7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I5R7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1XK (Subject of Investigation/LOI)
Query on 1XK

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
Q [auth C],
V [auth D]
4-[(3S)-3-cyclopropyl-3-(hydroxymethyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide
C26 H28 F N5 O3
SGTQLZKTLHEFII-AREMUKBSSA-N
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
R [auth C]HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
PRO
Query on PRO

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
P [auth C],
U [auth D]
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
BU1
Query on BU1

Download Ideal Coordinates CCD File 
G [auth A]1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
M [auth B]
N [auth B]
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
W [auth D],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.02α = 90
b = 140.6β = 90
c = 187.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaPR32713

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-04
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection
  • Version 1.2: 2024-07-31
    Changes: Database references, Structure summary