2ZCE

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

Structural Biology Knowledgebase: 2ZCE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZCE

Classification: LIGASE

Total Structure Weight: 34154.52

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

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
 
JSmol
MG
Query on MG

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

A PYRROLYSINE
C12 H21 N3 O3
ZFOMKMMPBOQKMC-KXUCPTDWSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.190
  • Space Group: P 64
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.50 α = 90.00
b = 104.50 β = 90.00
c = 70.85 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-08
  • Released Date: 2008-04-22
  • Deposition author(s): Yanagisawa, T., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

  • 2014-02-05
    Type: Other | Details: recover REVDAT
  • 2014-01-22
    Type: Non-polymer description | Details: replace PYH with PYL
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4