3D7V Apoptosis date May 22, 2008
title Crystal Structure Of Mcl-1 In Complex With An Mcl-1 Selectiv Ligand
authors E.F.Lee, P.E.Czabotar, P.M.Colman, W.D.Fairlie
compound source
Molecule: Induced Myeloid Leukemia Cell Differentiation Pro 1;
Chain: A
Fragment: Bcl-2 Like Domain, Myeloid Cell Leukemia 1
Synonym: Bcl-2-Related Protein Eatmcl1, Mcl1eat
Engineered: Yes
Other_details: Fusion Protein Consists Of The N-Terminal Ex Tags (Gplgs), Residues 171-208 (Uniprot Residues 152-189) F Induced Myeloid Leukemia Cell Differentiation Protein Mcl-1 (Mouse) And Residues 209-327 From Induced Myeloid Leukemia Differentiation Protein Mcl-1 (Human);
Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mouse, Human
Organism_taxid: 10090, 9606
Gene: Mcl1
Expression_system: Escherichia Coli
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p-3

Molecule: Bcl-2-Like Protein 11
Chain: B
Fragment: Bim Bh3
Synonym: Bcl2-Interacting Mediator Of Cell Death
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Other_details: Synthetic Peptide
symmetry Space Group: I 2 2 2
R_factor 0.192 R_Free 0.241
length a length b length c angle alpha angle beta angle gamma
51.171 69.635 120.654 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.03 Å
ligand ZN enzyme

Primary referenceA novel BH3 ligand that selectively targets Mcl-1 reveals that apoptosis can proceed without Mcl-1 degradation., Lee EF, Czabotar PE, van Delft MF, Michalak EM, Boyle MJ, Willis SN, Puthalakath H, Bouillet P, Colman PM, Huang DC, Fairlie WD, J Cell Biol. 2008 Jan 28;180(2):341-55. Epub 2008 Jan 21. PMID:18209102
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (3d7v.pdb1.gz) 31 Kb
  • LPC: Ligand-Protein Contacts for 3D7V
  • CSU: Contacts of Structural Units for 3D7V
  • Likely Quarternary Molecular Structure file(s) for 3D7V
  • Structure Factors (107 Kb)
  • Retrieve 3D7V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D7V from S2C, [Save to disk]
  • Re-refined 3d7v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D7V 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 3D7V
  • 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 3D7V, from MSDmotif at EBI
  • Fold representative 3d7v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d7v] [3d7v_B] [3d7v_A]
  • SWISS-PROT database: [O43521] [Q07820]
  • Belongs to the pro-apoptotic bcl-2-family protein bim (bim) family according to TCDB.
  • Domain organization of [B2L11_HUMAN] [MCL1_HUMAN] by SWISSPFAM
  • Domain found in 3D7V: [BCL ] by SMART
  • Other resources with information on 3D7V
  • Community annotation for 3D7V 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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