4JY6 Crystal structure of human Fab PGT123, a broadly reactive and potent HIV-1 neutralizing antibody date
authors Julien, J.P., Diwanji, D.C., Burton, D.R., Wilson, I.A.
compound source
symmetry
R_factor
R_Free 0.2652
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.50
ligand GOL, ZN enzyme
Primary referenceBroadly Neutralizing Antibody PGT121 Allosterically Modulates CD4 Binding via Recognition of the HIV-1 gp120 V3 Base and Multiple Surrounding Glycans., Julien JP, Sok D, Khayat R, Lee JH, Doores KJ, Walker LM, Ramos A, Diwanji DC, Pejchal R, Cupo A, Katpally U, Depetris RS, Stanfield RL, McBride R, Marozsan AJ, Paulson JC, Sanders RW, Moore JP, Burton DR, Poignard P, Ward AB, Wilson IA, PLoS Pathog. 2013 May;9(5):e1003342. doi: 10.1371/journal.ppat.1003342. Epub 2013, May 2. PMID:23658524
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (279 Kb) [Save to disk]
  • Biological Unit Coordinates (4jy6.pdb1.gz) 139 Kb
  • Biological Unit Coordinates (4jy6.pdb2.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 4JY6
  • CSU: Contacts of Structural Units for 4JY6
  • Structure Factors (363 Kb)
  • Retrieve 4JY6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JY6 from S2C, [Save to disk]
  • Re-refined 4jy6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4JY6 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 4JY6
  • 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
  • 3D motif for 4JY6, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jy6_C] [4jy6_A] [4jy6_D] [4jy6] [4jy6_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4JY6: [IG_like] [IGv ] by SMART
    • Other resources with information on 4JY6
  • Community annotation for 4JY6 at PDBWiki (http://pdbwiki.org)

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