2PME Ligase date Apr 21, 2007
title The Apo Crystal Structure Of The Glycyl-Trna Synthetase
authors W.Xie
compound source
Molecule: Glycyl-Trna Synthetase
Chain: A
Synonym: Glycine--Trna Ligase, Glyrs
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gars
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21-De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a(+)
symmetry Space Group: P 43 21 2
R_factor 0.230 R_Free 0.271
length a length b length c angle alpha angle beta angle gamma
91.742 91.742 247.176 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
enzyme Ligase E.C. BRENDA

Primary referenceLong-range structural effects of a Charcot-Marie-Tooth disease-causing mutation in human glycyl-tRNA synthetase., Xie W, Nangle LA, Zhang W, Schimmel P, Yang XL, Proc Natl Acad Sci U S A. 2007 Jun 12;104(24):9976-81. Epub 2007 Jun 1. PMID:17545306
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (2pme.pdb1.gz) 172 Kb
  • CSU: Contacts of Structural Units for 2PME
  • Likely Quarternary Molecular Structure file(s) for 2PME
  • Structure Factors (170 Kb)
  • Retrieve 2PME in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PME from S2C, [Save to disk]
  • Re-refined 2pme structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PME in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2PME
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2PME, from MSDmotif at EBI
  • Fold representative 2pme from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pme_A] [2pme]
  • SWISS-PROT database: [P41250]
  • Domain organization of [SYG_HUMAN] by SWISSPFAM
  • Domain found in 2PME: [WHEP-TRS ] by SMART
  • Other resources with information on 2PME
  • Community annotation for 2PME at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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