1YYL crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b date
authors Huang, C.C., Stricher, F., Martin, L., Decker, J.M., Majeed, S., Barthe, P., Hendrickson, W.A., Robinson, J., Roumestand, C., Sodroski, J., Wyatt, R., Shaw, G.M., Vita, C., Kwong, P.D.
compound source
symmetry
R_factor
R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.75
ligand BIF, MPT, NAG, VLM enzyme
related structures by homologous chain: 1F6L, 1GC1, 1H8O, 1HZH, 1RZK, 1UWG
Gene
Ontology
ChainFunctionProcessComponent
P, G


Primary referenceScorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth., Huang CC, Stricher F, Martin L, Decker JM, Majeed S, Barthe P, Hendrickson WA, Robinson J, Roumestand C, Sodroski J, Wyatt R, Shaw GM, Vita C, Kwong PD, Structure. 2005 May;13(5):755-68. PMID:15893666
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (254 Kb) [Save to disk]
  • Biological Unit Coordinates (1yyl.pdb1.gz) 127 Kb
  • Biological Unit Coordinates (1yyl.pdb2.gz) 126 Kb
  • LPC: Ligand-Protein Contacts for 1YYL
  • CSU: Contacts of Structural Units for 1YYL
  • Likely Quarternary Molecular Structure file(s) for 1YYL
  • Structure Factors (593 Kb)
  • Retrieve 1YYL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YYL from S2C, [Save to disk]
  • Re-refined 1yyl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1YYL 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 1YYL
  • 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 1YYL, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yyl_Q] [1yyl] [1yyl_G] [1yyl_S] [1yyl_H] [1yyl_L] [1yyl_M] [1yyl_R] [1yyl_P]
  • SWISS-PROT database: [P35961]
  • Domain organization of [ENV_HV1Y2] by SWISSPFAM
  • Domains found in 1YYL: [IG_like] [IGv ] by SMART
    • Other resources with information on 1YYL
  • Community annotation for 1YYL at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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