4BPJ Apoptosis date May 27, 2013
title Mcl-1 Bound To Alpha Beta Puma Bh3 Peptide 3
authors B.J.Smith, E.F.Lee, J.W.Checco, S.H.Gellman, W.D.Fairlie
compound source
Molecule: Fusion Protein Consisting Of Induced Myeloid Leuk Differentiation Protein Mcl-1 Homolog;
Chain: A
Fragment: Fusion Protein Of Mouse Mcl-1, Residues 152-189 A Mcl-1 Residues, 209-327;
Synonym: Bcl-2-Related Protein Eatmcl1, Bcl-2-Like Protein L-3, Bcl-2-Related Protein Eatmcl1, Mcl1eat, Mcl-1 Bcl-2- Protein 3, Bcl2-L-3, Bcl-2-Related Protein Eatmcl1, Mcl1e
Engineered: Yes
Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: House Mouse, Human
Organism_taxid: 10090, 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p3

Molecule: Alpha Beta Bh3-Peptide
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.199 R_Free 0.230
length a length b length c angle alpha angle beta angle gamma
78.458 60.260 44.804 90.00 118.47 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand B3A, B3D, B3Q, CL, DAL, HR7, NH2, ZN enzyme

Primary referenceStructure-guided rational design of alpha/beta-peptide foldamers with high affinity for BCL-2 family prosurvival proteins., Smith BJ, Lee EF, Checco JW, Evangelista M, Gellman SH, Fairlie WD, Chembiochem. 2013 Sep 2;14(13):1564-72. doi: 10.1002/cbic.201300351. Epub 2013, Aug 8. PMID:23929624
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (4bpj.pdb1.gz) 130 Kb
  • LPC: Ligand-Protein Contacts for 4BPJ
  • CSU: Contacts of Structural Units for 4BPJ
  • Structure Factors (290 Kb)
  • Retrieve 4BPJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BPJ from S2C, [Save to disk]
  • Re-refined 4bpj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BPJ 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 4BPJ
  • 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 4BPJ, from MSDmotif at EBI
  • Fold representative 4bpj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bpj_A] [4bpj] [4bpj_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4BPJ: [BCL ] by SMART
  • Other resources with information on 4BPJ
  • Community annotation for 4BPJ at PDBWiki (http://pdbwiki.org)

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