2Q5H Ligase date Jun 01, 2007
title Crystal Structure Of Apo-Wildtype Glycyl-Trna Synthetase
authors M.Z.Cader, J.Ren, P.A.James, L.E.Bird, K.Talbot, D.K.Stammers, Oxf Protein Production Facility (Oppf)
compound source
Molecule: Glycyl-Trna Synthetase
Chain: A
Fragment: Residues 55-739
Synonym: Glycine-Trna Ligase, Glyrs
Ec: 6.1.1.14
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: Pet22b
symmetry Space Group: P 43 21 2
R_factor 0.205 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.530 92.530 246.860 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand
enzyme Ligase E.C.6.1.1.14 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of human wildtype and S581L-mutant glycyl-tRNA synthetase, an enzyme underlying distal spinal muscular atrophy., Cader MZ, Ren J, James PA, Bird LE, Talbot K, Stammers DK, FEBS Lett. 2007 Jun 26;581(16):2959-2964. Epub 2007 May 29. PMID:17544401
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (2q5h.pdb1.gz) 170 Kb
  • CSU: Contacts of Structural Units for 2Q5H
  • Likely Quarternary Molecular Structure file(s) for 2Q5H
  • Structure Factors (177 Kb)
  • Retrieve 2Q5H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Q5H from S2C, [Save to disk]
  • Re-refined 2q5h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Q5H 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 2Q5H
  • 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 2Q5H, from MSDmotif at EBI
  • Fold representative 2q5h from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2q5h_A] [2q5h]
  • SWISS-PROT database: [P41250]
  • Domain organization of [SYG_HUMAN] by SWISSPFAM
  • Domain found in 2Q5H: [WHEP-TRS ] by SMART
  • Other resources with information on 2Q5H
  • Community annotation for 2Q5H 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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