5EKD

Human mitochondrial tryptophanyl-tRNA synthetase bound by indolmycin and Mn*ATP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Binding of Mg2+ATP Enhances Inhibition of Human Mitochondrial Tryptophanyl-tRNA Synthetase by Indolmycin

Williams, T.L.Carter Jr., C.W.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptophan--tRNA ligase, mitochondrial
A, B
343Homo sapiensMutation(s): 0 
Gene Names: WARS2
EC: 6.1.1.2
Find proteins for Q9UGM6 (Homo sapiens)
Go to Gene View: WARS2
Go to UniProtKB:  Q9UGM6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
5BX
Query on 5BX

Download SDF File 
Download CCD File 
A, B
(5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4(5H)-one
Indolemycin, Indolmycin
C14 H15 N3 O2
GNTVWGDQPXCYBV-PELKAZGASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 58.289α = 90.00
b = 78.087β = 96.55
c = 153.996γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM40906

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-12-07
    Type: Structure summary
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence
  • Version 1.3: 2019-12-25
    Type: Author supporting evidence, Derived calculations