4YDV STRUCTURE OF THE ANTIBODY 7B2 THAT CAPTURES HIV-1 VIRIONS date
authors Nicely, N.I., IV, C.W.Pemble.
compound source
symmetry
R_factor
R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.70
ligand ACE, NH2 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, L


Primary referenceHuman Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques., Santra S, Tomaras GD, Warrier R, Nicely NI, Liao HX, Pollara J, Liu P, Alam SM, Zhang R, Cocklin SL, Shen X, Duffy R, Xia SM, Schutte RJ, Pemble Iv CW, Dennison SM, Li H, Chao A, Vidnovic K, Evans A, Klein K, Kumar A, Robinson J, Landucci G, Forthal DN, Montefiori DC, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Robb ML, Michael NL, Kim JH, Soderberg KA, Giorgi EE, Blair L, Korber BT, Moog C, Shattock RJ, Letvin NL, Schmitz JE, Moody MA, Gao F, Ferrari G, Shaw GM, Haynes BF, PLoS Pathog. 2015 Aug 3;11(8):e1005042. doi: 10.1371/journal.ppat.1005042., eCollection 2015 Aug. PMID:26237403
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (306 Kb) [Save to disk]
  • Biological Unit Coordinates (4ydv.pdb1.gz) 146 Kb
  • Biological Unit Coordinates (4ydv.pdb2.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 4YDV
  • CSU: Contacts of Structural Units for 4YDV
  • Structure Factors (223 Kb)
  • Retrieve 4YDV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YDV from S2C, [Save to disk]
  • Re-refined 4ydv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4YDV 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 4YDV
  • 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: [4ydv_Q] [4ydv_L] [4ydv_P] [4ydv_A] [4ydv_B] [4ydv] [4ydv_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YDV: [IG_like] [IGv ] by SMART
    • Other resources with information on 4YDV
  • Community annotation for 4YDV at PDBWiki (http://pdbwiki.org)

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