5VWY Apoptosis date May 23, 2017
title Bak Core Latch Dimer In Complex With Bim-H3pc-Rt
authors J.M.Brouwer, P.M.Colman, P.E.Czabotar
compound source
Molecule: Bcl-2 Homologous Antagonistkiller
Chain: A
Fragment: Unp Residues 23-186
Synonym: Apoptosis Regulator Bak,Bcl-2-Like Protein 7,Bcl2-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bak1, Bak, Bcl2l7, Cdn1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Bcl-2-Like Protein 11
Chain: B
Fragment: Unp Residues 141-166
Synonym: Bcl2-L-11,Bcl2-Interacting Mediator Of Cell Death
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.175 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.890 37.540 69.560 90.00 107.86 90.00
method X-Ray Diffractionresolution 1.56 Å
ligand 9R1, PO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceConversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design., Brouwer JM, Lan P, Cowan AD, Bernardini JP, Birkinshaw RW, van Delft MF, Sleebs BE, Robin AY, Wardak A, Tan IK, Reljic B, Lee EF, Fairlie WD, Call MJ, Smith BJ, Dewson G, Lessene G, Colman PM, Czabotar PE, Mol Cell. 2017 Nov 16;68(4):659-672.e9. doi: 10.1016/j.molcel.2017.11.001. PMID:29149594
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (5vwy.pdb1.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 5VWY
  • CSU: Contacts of Structural Units for 5VWY
  • Structure Factors (178 Kb)
  • Retrieve 5VWY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VWY from S2C, [Save to disk]
  • View 5VWY 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 5VWY
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vwy_A] [5vwy_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VWY
  • Community annotation for 5VWY at PDBWiki (http://pdbwiki.org)

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