5UD5

Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase bound to tRNA(Pyl)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.216

Literature

Macromolecules
Sequence Display for 5UD5

Classification: LIGASE / RNA

Total Structure Weight: 71569.46


Macromolecule Entities
Molecule Chains Length Organism Details
Pyrrolysine--tRNA ligase A, B 109 Methanosarcina mazei EC#: 6.1.1.26 IUBMB
Fragment: UNP residues 1-101
Gene Name(s): pylS MM_1445
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (70-MER) C, D 72 Methanosarcina mazei

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.216
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 72.28 α = 90.00
b = 72.28 β = 90.00
c = 238.97 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-12-23
  • Released Date: 2017-10-11
  • Deposition author(s): Suzuki, T., Soll, D.

Revision History

  • Version 1_0: 2017-10-11

    Type: Initial release

  • Version 1_1: 2017-10-25

    Type: Database references

  • Version 1_2: 2017-11-01

    Type: Database references

  • Version 1_3: 2017-12-06

    Type: Database references