2ZIO

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AlocLys-AMP and PNP

Structural Biology Knowledgebase: 2ZIO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.183

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZIO

Classification: Ligase

Total Structure Weight: 34082.88

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

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

A 5'-O-[(S)-({(2S)-2-amino-6-[(propoxycarbonyl)amino]hexanoyl}oxy)(hydroxy)phosphoryl]adenosine
NE-ALLYLOXYCARBONYL-L-LYSINE-5'-ADENOSINE MONOPHOSPHATE (Synonym)
C20 H32 N7 O10 P
FNGSPKAFCIGHDI-URQYDQELSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
2PN
Query on 2PN

A IMIDODIPHOSPHORIC ACID
H5 N O6 P2
GNGSOPFGGKKDQP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.183
  • Space Group: P 64
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.15 α = 90.00
b = 104.15 β = 90.00
c = 71.06 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