5X4S Viral Protein date Feb 14, 2017
title Structure Of The N-Terminal Domain (Ntd)Of Sars-Cov Spike Pr
authors Y.Yuan, Y.Zhang, J.Qi, Y.Shi, G.F.Gao
compound source
Molecule: Spike Glycoprotein
Chain: A
Fragment: Unp Residues 14-292
Synonym: S Glycoprotein,E2,Peplomer Protein
Engineered: Yes
 Organism_scientific: Human Sars Coronavirus
Organism_common: Sars-Cov
Organism_taxid: 227859
Strain: Bj01
Gene: S, 2
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
symmetry Space Group: P 61 2 2
R_factor 0.252 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.291 73.291 240.263 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand NAG enzyme
Primary referenceCryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains., Yuan Y, Cao D, Zhang Y, Ma J, Qi J, Wang Q, Lu G, Wu Y, Yan J, Shi Y, Zhang X, Gao GF, Nat Commun. 2017 Apr 10;8:15092. doi: 10.1038/ncomms15092. PMID:28393837
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (5x4s.pdb1.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 5X4S
  • CSU: Contacts of Structural Units for 5X4S
  • Structure Factors (329 Kb)
  • Retrieve 5X4S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5X4S from S2C, [Save to disk]
  • Re-refined 5x4s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5X4S 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 5X4S
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5x4s] [5x4s_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5X4S
  • Community annotation for 5X4S at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science