6B72 Viral Protein date Oct 03, 2017
title A Novel Hiv-1 Nef Dimer Interface Induced By A Single Octyl- Molecule
authors M.Wu, C.E.Augelli-Szafran, R.G.Ptak, T.E.Smithgall
compound source
Molecule: Protein Nef
Chain: A, B, C, D, E, F
Fragment: Unp Residues 57-207
Synonym: 3'Orf,Negative Factor,F-Protein
Engineered: Yes
 Organism_scientific: Human Immunodeficiency Virus Type 1 Gr Subtype B;
Organism_common: Isolate Arv2sf2
Organism_taxid: 11685
Gene: Nef
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 32 2 1
R_factor 0.233 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
109.577 109.577 247.040 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.20 Å
ligand BOG enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceA single beta-octyl glucoside molecule induces HIV-1 Nef dimer formation in the absence of partner protein binding., Wu M, Alvarado JJ, Augelli-Szafran CE, Ptak RG, Smithgall TE, PLoS One. 2018 Feb 7;13(2):e0192512. doi: 10.1371/journal.pone.0192512., eCollection 2018. PMID:29415006
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (267 Kb) [Save to disk]
  • Biological Unit Coordinates (6b72.pdb1.gz) 89 Kb
  • Biological Unit Coordinates (6b72.pdb2.gz) 88 Kb
  • Biological Unit Coordinates (6b72.pdb3.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 6B72
  • CSU: Contacts of Structural Units for 6B72
  • Structure Factors (833 Kb)
  • Retrieve 6B72 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6B72 from S2C, [Save to disk]
    • View 6B72 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 6B72
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6b72_A] [6b72_B] [6b72_F] [6b72_E] [6b72_C] [6b72_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6B72
  • Community annotation for 6B72 at PDBWiki (http://pdbwiki.org)

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