3VQY

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and AMPPNP (form 2)

Structural Biology Knowledgebase: 3VQY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VQY

Classification: LIGASE

Total Structure Weight: 34145.52

Macromolecule Entities
Molecule Chains Length Organism Details
Pyrrolysine--tRNA ligase A 291 Methanosarcina mazei EC#: 6.1.1.26 IUBMB

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

A PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LBY
Query on LBY

A N~6~-(tert-butoxycarbonyl)-L-lysine
C11 H22 N2 O4
VVQIIIAZJXTLRE-QMMMGPOBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.197
  • Space Group: P 64
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 103.36 α = 90.00
b = 103.36 β = 90.00
c = 70.91 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-02
  • Released Date: 2013-01-02
  • Deposition author(s): Yanagisawa, T., Sumida, T., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

  • 2013-09-04
    Type: Citation | Details: Citation update