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 Diffraction	resolution	1.78 Å
note	3FDL is a representative structure
Gene Ontology	Chain Function Process Component A protein binding protein kinase binding protein heterodimerization a... cytokinesis ovarian follicle development... in utero embryonic developme... release of cytochrome c from... apoptotic process mitotic cell cycle checkpoin... germ cell development spermatogenesis cell proliferation positive regulation of cell ... male gonad development negative regulation of survi... apoptotic mitochondrial chan... response to radiation fertilization response to virus response to cytokine stimulu... nucleotide-binding domain, l... growth positive regulation of apopt... negative regulation of apopt... negative regulation of neuro... innate immune response response to cycloheximide regulation of mitochondrial ... regulation of mitochondrial ... cellular process regulating ... cellular response to amino a... cellular response to alkaloi... cellular response to gamma r... negative regulation of estab... negative regulation of relea... intrinsic apoptotic signalin... positive regulation of intri... intracellular nucleus cytoplasm mitochondrion mitochondrial outer membrane... centrosome microtubule organizing cente... cytosol cytoskeleton membrane integral to membrane nuclear membrane mitochondrial membrane mitochondrial part Bcl-2 family protein complex...
Primary reference	High-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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [3fdl_B] 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)

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