5GYQ Viral Protein date Sep 23, 2016
title Putative Receptor-Binding Domain Of Bat-Derived Coronavirus Protein
authors C.Huang, J.Qi, G.F.Gao
compound source
Molecule: Spike Glycoprotein
Chain: A
Fragment: Unp Residues 355-521
Synonym: S Glycoprotein,E2,Peplomer Protein
Engineered: Yes
Organism_scientific: Bat Coronavirus Hku9
Organism_common: Btcov
Organism_taxid: 694006
Gene: S, 2
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 1 21 1
R_factor 0.170 R_Free 0.201
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.752 35.990 62.886 90.00 102.72 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand NAG enzyme
Primary referencePutative receptor-binding domain of bat-derived coronavirus HKU9 spike protein: evolution of betacoronavirus receptor binding motifs., Huang C, Qi J, Lu GW, Wang Q, Yuan Y, Wu Y, Zhang Y, Yan J, Gao GF, Biochemistry. 2016 Oct 3. PMID:27696819
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (5gyq.pdb1.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 5GYQ
  • CSU: Contacts of Structural Units for 5GYQ
  • Structure Factors (185 Kb)
  • Retrieve 5GYQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GYQ from S2C, [Save to disk]
  • Re-refined 5gyq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5GYQ 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 5GYQ
  • 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: [5gyq_A] [5gyq]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5GYQ
  • Community annotation for 5GYQ at PDBWiki (http://pdbwiki.org)

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