6T7K

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with NCP-26 and L-Proline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

Starting Model: experimental
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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 NCP-26 and L-Proline

Johansson, C.Wang, J.Tye, M.Payne, N.C.Mazitschek, R.Thompson, A.Arrowsmith, C.H.Bountra, C.Edwards, A.Oppermann, U.C.T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proline--tRNA ligase504Plasmodium 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MU5 (Subject of Investigation/LOI)
Query on MU5

Download Ideal Coordinates CCD File 
C [auth A]~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-(piperidin-1-ylcarbonylamino)pyrazine-2-carboxamide
C20 H23 N5 O2
AOICKOCLMIPLFS-UHFFFAOYSA-N
PRO
Query on PRO

Download Ideal Coordinates CCD File 
B [auth A]PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.999α = 90
b = 102.999β = 90
c = 126.831γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description