3FDL Apoptosis date Nov 26, 2008
title Bim Bh3 Peptide In Complex With Bcl-Xl
authors W.D.Fairlie, E.F.Lee, B.J.Smith, P.E.Czabotar, P.M.Colman
compound source
Molecule: Apoptosis Regulator Bcl-X
Chain: A
Fragment: Residue 1-209, Deletion Of Amino Acids 27 To 82
Synonym: Bcl-Xl, Bcl-2-Like 1 Protein
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bcl-X
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p3

Molecule: Bcl-2-Like Protein 11
Chain: B
Fragment: Bh3 Domain, Unp Residues 141-166
Synonym: Bcl2-Interacting Mediator Of Cell Death
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized
symmetry Space Group: C 1 2 1
R_factor 0.160 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.111 35.684 62.760 90.00 111.54 90.00
method X-Ray Diffractionresolution 1.78 Å
note 3FDL is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceHigh-Resolution Structural Characterization of a Helical alpha/beta-Peptide Foldamer Bound to the Anti-Apoptotic Protein Bcl-x(L)., Lee EF, Sadowsky JD, Smith BJ, Czabotar PE, Peterson-Kaufman KJ, Colman PM, Gellman SH, Fairlie WD, Angew Chem Int Ed Engl. 2009 Feb 19. PMID:19229915
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (37 Kb) [Save to disk]
  • Biological Unit Coordinates (3fdl.pdb1.gz) 33 Kb
  • Biological Unit Coordinates (3fdl.pdb2.gz) 64 Kb
  • CSU: Contacts of Structural Units for 3FDL
  • Likely Quarternary Molecular Structure file(s) for 3FDL
  • Structure Factors (215 Kb)
  • Retrieve 3FDL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FDL from S2C, [Save to disk]
  • Re-refined 3fdl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FDL 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 3FDL
  • 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 3FDL, from MSDmotif at EBI
  • Fold representative 3fdl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fdl_B] [3fdl_A] [3fdl]
  • SWISS-PROT database: [Q07817] [O43521]
  • Belongs to the bcl-2 (bcl-2) family according to TCDB.
  • Domain organization of [B2CL1_HUMAN] [B2L11_HUMAN] by SWISSPFAM
  • Domains found in 3FDL: [BCL] [BH4 ] by SMART
  • Alignments of the sequence of 3FDL with the sequences similar proteins can be viewed for 3FDL's classification [B2CL1_HUMAN] [B2L11_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [B2CL1_HUMAN] [B2L11_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3FDL
  • Community annotation for 3FDL 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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