2NL9 Apoptosis date Oct 19, 2006
title Crystal Structure Of The Mcl-1:Bim Bh3 Complex
authors P.E.Czabotar, P.M.Colman
compound source
Molecule: Fusion Protein Consisting Of Induced Myeloid Leuk Differentiation Protein Mcl-1 Homolog;
Chain: A
Fragment: Residues 171-208 And Residues 209-327
Engineered: Yes
Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mouse, Human
Organism_taxid: 10090, 9606
Gene: Mcl1
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
Synonym: Bcl2-Interacting Mediator Of Cell Death

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: I 2 2 2
R_factor 0.173 R_Free 0.203
length a length b length c angle alpha angle beta angle gamma
52.380 70.080 117.180 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.55 Å
ligand CL, MSE, ZN enzyme
note 2NL9 is a representative structure

Primary referenceStructural insights into the degradation of Mcl-1 induced by BH3 domains., Czabotar PE, Lee EF, van Delft MF, Day CL, Smith BJ, Huang DC, Fairlie WD, Hinds MG, Colman PM, Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6217-22. Epub 2007 Mar 27. PMID:17389404
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (2nl9.pdb1.gz) 33 Kb
  • Biological Unit Coordinates (2nl9.pdb2.gz) 130 Kb
  • Biological Unit Coordinates (2nl9.pdb3.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 2NL9
  • CSU: Contacts of Structural Units for 2NL9
  • Likely Quarternary Molecular Structure file(s) for 2NL9
  • Structure Factors (242 Kb)
  • Retrieve 2NL9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NL9 from S2C, [Save to disk]
  • Re-refined 2nl9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2NL9 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 2NL9
  • 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 2NL9, from MSDmotif at EBI
  • Fold representative 2nl9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2nl9_A] [2nl9] [2nl9_B]
  • SWISS-PROT database: [O43521] [Q07820] [P97287]
  • Belongs to the pro-apoptotic bcl-2-family protein bim (bim) family according to TCDB.
  • Domain organization of [B2L11_HUMAN] [MCL1_HUMAN] [MCL1_MOUSE] by SWISSPFAM
  • Domain found in 2NL9: [BCL ] by SMART
  • Other resources with information on 2NL9
  • Community annotation for 2NL9 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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