6OZ5

Escherichia coli tRNA synthetase in complex with compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report



Literature

Escherichia coli tRNA synthetase in complex with compound 3

Kahne, D.Baidin, V.Owens, T.W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligase alpha subunitAC332Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: pheSD8B36_10295
EC: 6.1.1.20
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligase beta subunitBD795Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: pheTD8B36_10300
EC: 6.1.1.20
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VB3
Query on VB3

Download CCD File 
A, C
2-({[(2S)-1-cyclohexylpropan-2-yl]amino}methyl)phenol
C16 H25 N O
IRWBEPDMVHOCPD-ZDUSSCGKSA-N
 Ligand Interaction
PGE
Query on PGE

Download CCD File 
D
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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B, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.775α = 90
b = 174.508β = 90
c = 252.548γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19-AI109764-05-8340

Revision History 

  • Version 1.0: 2020-11-18
    Type: Initial release