3RBB Viral Protein, Protein Binding date Mar 29, 2011
title Hiv-1 Nef Protein In Complex With Engineered Hck Sh3 Domain
authors F.A.Horenkamp, A.Schulte, M.Weyand, M.Geyer
compound source
Molecule: Protein Nef
Chain: A, C
Synonym: 3'Orf, Negative Factor, F-Protein, C-Terminal Core
Engineered: Yes
Mutation: Yes
Organism_scientific: Hiv-1 M:B_arv2sf2
Organism_common: Hiv-1
Organism_taxid: 11685
Strain: Sf2
Gene: Hiv-1 Nef, Nef
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-4t1 Tev

Molecule: Tyrosine-Protein Kinase Hck
Chain: B, D
Synonym: Hemopoietic Cell Kinase, P59-Hckp60-Hck
Ec: 2.7.10.2
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hck
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28b
symmetry Space Group: P 21 21 21
R_factor 0.204 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.190 90.880 169.530 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand EDO enzyme Transferase E.C.2.7.10.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceConformation of the dileucine based sorting motif in HIV-1 Nef revealed by intermolecular domain assembly., Horenkamp FA, Breuer S, Schulte A, Lulf S, Weyand M, Saksela K, Geyer M, Traffic. 2011 Apr 7. doi: 10.1111/j.1600-0854.2011.01205.x. PMID:21477083
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (3rbb.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (3rbb.pdb2.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 3RBB
  • CSU: Contacts of Structural Units for 3RBB
  • Structure Factors (415 Kb)
  • Retrieve 3RBB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RBB from S2C, [Save to disk]
  • Re-refined 3rbb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RBB 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 3RBB
  • 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 3RBB, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rbb_B] [3rbb_A] [3rbb_C] [3rbb_D] [3rbb]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3RBB: [SH3 ] by SMART
  • Other resources with information on 3RBB
  • Community annotation for 3RBB 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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