2ZIN

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and an ATP analogue

Structural Biology Knowledgebase: 2ZIN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZIN

Classification: Ligase

Total Structure Weight: 34207.58

Macromolecule Entities
Molecule Chains Length Organism Details
Pyrrolysyl-tRNA synthetase A 291 Methanosarcina mazei EC#: 6.1.1.26 IUBMB
Mutation: E444G
Gene Name(s): pylS MM_1445

Small Molecules
Ligands 4 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
 
JSmol
EDO
Query on EDO

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

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.190
  • Space Group: P 64
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.71 α = 90.00
b = 104.71 β = 90.00
c = 70.55 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-02-19
  • Released Date: 2008-12-02
  • Deposition author(s): Yanagisawa, T., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4