5XIX Ligase date Apr 28, 2017
title The Canonical Domain Of Human Asparaginyl-Trna Synthetase
authors J.S.Park, B.W.Han
compound source
Molecule: Asparagine--Trna Ligase, Cytoplasmic
Chain: A, B, C, D
Fragment: Unp Residues 98-548
Synonym: Asparaginyl-Trna Synthetase,Asnrs
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nars
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.177 R_Free 0.229
length a length b length c angle alpha angle beta angle gamma
113.350 127.103 163.475 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand GOL enzyme Ligase E.C. BRENDA
A, D, C, B

Primary referenceUnique N-terminal extension domain of human asparaginyl-tRNA synthetase elicits CCR3-mediated chemokine activity., Park JS, Park MC, Lee KY, Goughnour PC, Jeong SJ, Kim HS, Kim HJ, Lee BJ, Kim S, Han BW, Int J Biol Macromol. 2018 Dec;120(Pt A):835-845. doi:, 10.1016/j.ijbiomac.2018.08.171. Epub 2018 Aug 30. PMID:30171954
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (309 Kb) [Save to disk]
  • Biological Unit Coordinates (5xix.pdb1.gz) 153 Kb
  • Biological Unit Coordinates (5xix.pdb2.gz) 154 Kb
  • LPC: Ligand-Protein Contacts for 5XIX
  • CSU: Contacts of Structural Units for 5XIX
  • Structure Factors (808 Kb)
  • Retrieve 5XIX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XIX from S2C, [Save to disk]
  • View 5XIX 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 5XIX
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5xix from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xix_A] [5xix_B] [5xix_D] [5xix_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5XIX
  • Community annotation for 5XIX at PDBWiki (http://pdbwiki.org)

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