5V59 Ligase date Mar 13, 2017
title Crystal Structure Of Catalytic Fragment Of Human Alars In Co Aze-Sa
authors H.Zhou, Y.Song, P.Schimmel
compound source
Molecule: Alanine--Trna Ligase, Cytoplasmic
Chain: A
Fragment: Catalytic Domain (Unp Residues 1-455)
Synonym: Alanyl-Trna Synthetase, Alars, Renal Carcinoma Ant Ren-42;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aars
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.180 R_Free 0.215
length a length b length c angle alpha angle beta angle gamma
108.330 67.270 86.350 90.00 136.23 90.00
method X-Ray Diffractionresolution 2.03 Å
enzyme Ligase E.C. BRENDA

Primary referenceDouble mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid., Song Y, Zhou H, Vo MN, Shi Y, Nawaz MH, Vargas-Rodriguez O, Diedrich JK, Yates JR, Kishi S, Musier-Forsyth K, Schimmel P, Nat Commun. 2017 Dec 22;8(1):2281. doi: 10.1038/s41467-017-02201-z. PMID:29273753
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (136 Kb) [Save to disk]
  • Biological Unit Coordinates (5v59.pdb1.gz) 131 Kb
  • CSU: Contacts of Structural Units for 5V59
  • Structure Factors (1303 Kb)
  • Retrieve 5V59 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V59 from S2C, [Save to disk]
  • View 5V59 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 5V59
  • 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 5v59 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v59_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5V59
  • Community annotation for 5V59 at PDBWiki (http://pdbwiki.org)

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