4JY5 Crystal structure of human Fab PGT122, 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 0.2424
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.75
ligand GOL 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] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (4jy5.pdb1.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 4JY5
  • CSU: Contacts of Structural Units for 4JY5
  • Structure Factors (551 Kb)
  • Retrieve 4JY5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JY5 from S2C, [Save to disk]
  • Re-refined 4jy5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4JY5 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 4JY5
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4JY5, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jy5] [4jy5_L] [4jy5_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4JY5: [IG_like] [IGv ] by SMART
    • Other resources with information on 4JY5
  • Community annotation for 4JY5 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