4CH3

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

Structural Biology Knowledgebase: 4CH3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.176

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4CH3

Classification: LIGASE

Total Structure Weight: 34296.63

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

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

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
YLB
Query on YLB

A 5'-O-({[(2R)-2-amino-6-(butanoylamino)hexanoyl]oxy}phosphinato)adenosine
C20 H32 N7 O9 P
OAECZBFMQNITMX-JCQVVMGJSA-M
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.176
  • Space Group: P 64
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 105.26 α = 90.00
b = 105.26 β = 90.00
c = 71.38 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