6VYB Viral Protein date Feb 25, 2020
title Sars-Cov-2 Spike Ectodomain Structure (Open State)
authors A.C.Walls, Y.J.Park, M.A.Tortorici, A.Wall, Seattle Structural G Center For Infectious Disease (Ssgcid), A.T.Mcguire, D.Veesle
compound source
Molecule: Spike Glycoprotein
Chain: A, B, C
Fragment: Ectodomain
Synonym: S Glycoprotein,E2,Peplomer Protein
Engineered: Yes
Organism_scientific: Severe Acute Respiratory Syndrome Coro 2;
Organism_common: 2019-Ncov
Organism_taxid: 2697049
Gene: S, 2
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.20 Å
ligand NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (453 Kb) [Save to disk]
  • Biological Unit Coordinates (6vyb.pdb1.gz) 437 Kb
  • LPC: Ligand-Protein Contacts for 6VYB
  • CSU: Contacts of Structural Units for 6VYB
  • Retrieve 6VYB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6VYB from S2C, [Save to disk]
  • View 6VYB 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 6VYB
  • 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 6vyb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6vyb_C] [6vyb_A] [6vyb_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6VYB
  • Community annotation for 6VYB at PDBWiki (http://pdbwiki.org)

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