4CH6

Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propargyloxycarbonyl lysine

Structural Biology Knowledgebase: 4CH6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.174

Literature

Macromolecules
Sequence Display for 4CH6

Classification: LIGASE

Total Structure Weight: 34308.57

Macromolecule Entities
Molecule Chains Length Organism Details
PYRROLYSINE--TRNA LIGASE A 291 Methanosarcina mazei EC#: 6.1.1.26 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 185-454
Gene Name(s): pylS MM_1445
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
YLA
Query on YLA

A (S)-2-amino-6-(((prop-2-yn-1-yloxy)carbonyl)amino)hexanoic (((2R,3S,4R,5R)- 5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran- 2-yl)methyl phosphoric)anhydride
C20 H28 N7 O10 P
BXXVGWFYYCXKTG-AJKMGBEJSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.174
  • Space Group: P 64
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.93 α = 90.00
b = 104.93 β = 90.00
c = 70.96 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-11-28
  • Released Date: 2014-03-19
  • Deposition author(s): Fluegel, V., Vrabel, M., Schneider, S.

Revision History

  • 2014-05-07
    Type: Citation | Details: JRNL