2JBY Apoptosis date Dec 14, 2006
title A Viral Protein Unexpectedly Mimics The Structure And Functi Survival Bcl-2
authors M.Kvansakul, M.F.Van Delft, E.F.Lee, J.M.Gulbis, W.D.Fairlie, D.C P.M.Colman
compound source
Molecule: M11l Protein
Chain: A
Fragment: Residues 1-132
Synonym: Apoptosis Regulator M11l, M11l
Engineered: Yes
Organism_scientific: Myxoma Virus
Organism_taxid: 10273
Strain: Lausanne
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_variant: Plys
Expression_system_vector_type: Plasmid
Expression_system_vector: Pduet

Molecule: Bcl-2 Homologous Antagonistkiller 2
Chain: B
Fragment: Bh3 Domain, Residues 67-92
Synonym: Apoptosis Regulator Bak-2, Bak
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 41 21 2
R_factor 0.287 R_Free 0.292
length a length b length c angle alpha angle beta angle gamma
69.187 69.187 120.601 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.41 Å
ligand NA enzyme


Primary referenceA structural viral mimic of prosurvival Bcl-2: a pivotal role for sequestering proapoptotic Bax and Bak., Kvansakul M, van Delft MF, Lee EF, Gulbis JM, Fairlie WD, Huang DC, Colman PM, Mol Cell. 2007 Mar 23;25(6):933-42. PMID:17386268
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (2jby.pdb1.gz) 26 Kb
  • LPC: Ligand-Protein Contacts for 2JBY
  • CSU: Contacts of Structural Units for 2JBY
  • Likely Quarternary Molecular Structure file(s) for 2JBY
  • Structure Factors (82 Kb)
  • Retrieve 2JBY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2JBY from S2C, [Save to disk]
  • Re-refined 2jby structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2JBY 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 2JBY
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2JBY, from MSDmotif at EBI
  • Fold representative 2jby from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2jby] [2jby_A] [2jby_B]
  • SWISS-PROT database: [Q16611] [Q85295]
  • Belongs to the bcl-2 (bcl-2) family according to TCDB.
  • Domain organization of [BAK_HUMAN] [Q85295_9POXV] by SWISSPFAM
  • Other resources with information on 2JBY
  • Community annotation for 2JBY 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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