4ZYA Ligase date May 21, 2015
title The N-Terminal Extension Domain Of Human Asparaginyl-Trna Sy
authors J.S.Park, M.C.Park, P.Goughnour, H.S.Kim, S.J.Kim, H.J.Kim, S.H.Ki
compound source
Molecule: Asparagine--Trna Ligase, Cytoplasmic
Chain: A, B
Fragment: Unp Residues 4-77
Synonym: Asparaginyl-Trna Synthetase,Asnrs
Ec: 6.1.1.22
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 65
R_factor 0.206 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
32.626 32.626 215.921 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.65 Å
ligand CL, GOL, MSE, ZN enzyme Ligase E.C.6.1.1.22 BRENDA
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] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (4zya.pdb1.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 4ZYA
  • CSU: Contacts of Structural Units for 4ZYA
  • Structure Factors (218 Kb)
  • Retrieve 4ZYA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4ZYA from S2C, [Save to disk]
  • Re-refined 4zya structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4ZYA 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 4ZYA
  • 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 4zya from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4zya_B] [4zya] [4zya_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4ZYA
  • Community annotation for 4ZYA at PDBWiki (http://pdbwiki.org)

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