5THH Ligase date Sep 29, 2016
title Crystal Structure Of A Human Tyrosyl-Trna Synthetase Mutant
authors D.Blocquel, X.L.Yang
compound source
Molecule: Tyrosine--Trna Ligase, Cytoplasmic
Chain: A
Synonym: Tyrosyl-Trna Synthetase,Tyrrs
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Yars
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
symmetry Space Group: P 2 21 21
R_factor 0.178 R_Free 0.219
length a length b length c angle alpha angle beta angle gamma
35.238 75.705 163.510 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.96 Å
ligand TYR enzyme Ligase E.C. BRENDA

Primary referenceAlternative stable conformation capable of protein misinteraction links tRNA synthetase to peripheral neuropathy., Blocquel D, Li S, Wei N, Daub H, Sajish M, Erfurth ML, Kooi G, Zhou J, Bai G, Schimmel P, Jordanova A, Yang XL, Nucleic Acids Res. 2017 May 22. doi: 10.1093/nar/gkx455. PMID:28531329
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (123 Kb) [Save to disk]
  • Biological Unit Coordinates (5thh.pdb1.gz) 234 Kb
  • LPC: Ligand-Protein Contacts for 5THH
  • CSU: Contacts of Structural Units for 5THH
  • Structure Factors (524 Kb)
  • Retrieve 5THH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5THH from S2C, [Save to disk]
  • Re-refined 5thh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5THH 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 5THH
  • 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
  • Fold representative 5thh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5thh] [5thh_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5THH
  • Community annotation for 5THH at PDBWiki (http://pdbwiki.org)

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