4BPK Apoptosis date May 27, 2013
title Bcl-Xl Bound To Alpha Beta Puma Bh3 Peptide 5
authors B.J.Smith, E.F.Lee, J.W.Checco, S.H.Gellman, W.D.Fairlie
compound source
Molecule: Bcl-2-Like Protein 1
Chain: A, B
Fragment: Residues 1-26,83-209
Synonym: Bcl2-L-1, Apoptosis Regulator Bcl-X, Bcl-Xl
Engineered: Yes
Other_details: Bcl-Xl Without C-Terminal Domain Or Loop Bet And Alpha 2 Helices;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 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: C, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.219 R_Free 0.252
length a length b length c angle alpha angle beta angle gamma
65.175 72.133 80.579 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.76 Å
ligand ACE, AHP, B3A, B3D, B3E, B3Q, CD, EDO, HR7, HT7, NH2 enzyme
A, B

D, C

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] (137 Kb) [Save to disk]
  • Biological Unit Coordinates (4bpk.pdb1.gz) 128 Kb
  • LPC: Ligand-Protein Contacts for 4BPK
  • CSU: Contacts of Structural Units for 4BPK
  • Structure Factors (705 Kb)
  • Retrieve 4BPK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BPK from S2C, [Save to disk]
  • Re-refined 4bpk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BPK 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 4BPK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4BPK, from MSDmotif at EBI
  • Fold representative 4bpk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bpk_B] [4bpk_D] [4bpk_A] [4bpk_C] [4bpk]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4BPK: [BCL] [BH4 ] by SMART
  • Other resources with information on 4BPK
  • Community annotation for 4BPK at PDBWiki (http://pdbwiki.org)

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