5K79 Antiviral Protein date May 25, 2016
title Structure And Anti-Hiv Activity Of Cyt-Cvnh, A New Cyanoviri Homolog
authors E.Matei, R.Basu, W.Furey, J.Shi, C.Calnan, C.Aiken, A.M.Gronenborn
compound source
Molecule: Cyanovirin-N Domain Protein
Chain: A, B
Fragment: Residues 32-139
Engineered: Yes
Organism_scientific: Cyanothece Sp. (Strain Pcc 7424)
Organism_taxid: 65393
Strain: Pcc 7424
Gene: Pcc7424_1905
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b
symmetry Space Group: P 21 21 2
R_factor 0.202 R_Free 0.233
length a length b length c angle alpha angle beta angle gamma
93.840 74.396 36.499 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand EDO, PEG enzyme
Gene PCC7424
Primary referenceStructure and Glycan Binding of a New Cyanovirin-N Homolog., Matei E, Basu R, Furey W, Shi J, Calnan C, Aiken C, Gronenborn AM, J Biol Chem. 2016 Jul 7. pii: jbc.M116.740415. PMID:27402833
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (5k79.pdb1.gz) 20 Kb
  • Biological Unit Coordinates (5k79.pdb2.gz) 20 Kb
  • LPC: Ligand-Protein Contacts for 5K79
  • CSU: Contacts of Structural Units for 5K79
  • Structure Factors (241 Kb)
  • Retrieve 5K79 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5K79 from S2C, [Save to disk]
  • Re-refined 5k79 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5K79 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 5K79
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5k79 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5k79_B] [5k79] [5k79_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5K79: [CVNH ] by SMART
  • Other resources with information on 5K79
  • Community annotation for 5K79 at PDBWiki (http://pdbwiki.org)

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