1DF5 Viral Protein date Nov 17, 1999
title Interactions Between Hiv-1 Gp41 Core And Detergents And Thei Implications For Membrane Fusion
authors W.Shu, H.Ji, M.Lu
compound source
Molecule: Hiv-1 Envelope Glycoprotein Gp41
Chain: A
Fragment: Residues 1 - 34 And 41 - 68 Connected By A Six-Re Linker (Ser-Gly-Gly-Arg-Gly-Gly);
Engineered: Yes
 Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Recombinant Gp41 With Linker (Ser-Gly-Gly- A Gly) Between Two Fragments
symmetry Space Group: I 21 3
R_factor 0.183 R_Free 0.315
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.770 72.770 72.770 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
related structures by homologous chain: 1ENV, 2EZO
Primary referenceInteractions between HIV-1 gp41 core and detergents and their implications for membrane fusion., Shu W, Ji H, Lu M, J Biol Chem 2000 Jan 21;275(3):1839-45. PMID:10636883
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (16 Kb) [Save to disk]
  • Biological Unit Coordinates (1df5.pdb1.gz) 34 Kb
  • CSU: Contacts of Structural Units for 1DF5
  • Likely Quarternary Molecular Structure file(s) for 1DF5
  • Retrieve 1DF5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DF5 from S2C, [Save to disk]
    • View 1DF5 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 1DF5
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1DF5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1df5a_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1df5_A] [1df5]
  • SWISS-PROT database: [P04578]
  • Belongs to the human immunodeficiency virus type 1 (hiv-1) fusion peptide (hiv-fp) family according to TCDB.
  • Domain organization of [ENV_HV1H2] by SWISSPFAM
    • Other resources with information on 1DF5
  • Community annotation for 1DF5 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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