2VM6 Immune System date Jan 23, 2008
title Human Bcl2-A1 In Complex With Bim-Bh3 Peptide
authors M.D.Herman, L.Lehtio, C.H.Arrowsmith, H.Berglund, R.D.Busam, R.Co L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Ham I.Johansson, A.Kallas, T.Karlberg, T.Kotenyova, M.Moche, M.E.Nil T.Nyman, C.Persson, J.Sagemark, L.Svensson, A.G.Thorsell, L.Tres S.Van Den Berg, J.Weigelt, M.Welin, P.Nordlund, Structural Geno Consortium (Sgc)
compound source
Molecule: Bcl-2-Related Protein A1
Chain: A
Fragment: Residues 1-149
Synonym: Protein Bfl-1, Hemopoietic-Specific Early Response Protein Grs, Bcl-2a1, A1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3) R3 Prare
Expression_system_plasmid: Pnic-Bsa4

Molecule: Bcl-2-Like Protein 11
Chain: B
Fragment: Residues 141-165
Synonym: Bcl2-Interacting Mediator Of Cell Death
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3) R3 Prare
Expression_system_plasmid: Pnic-Bsa4
symmetry Space Group: H 3 2
R_factor 0.194 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.800 70.800 208.800 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCompleting the family portrait of the anti-apoptotic Bcl-2 proteins: crystal structure of human Bfl-1 in complex with Bim., Herman MD, Nyman T, Welin M, Lehtio L, Flodin S, Tresaugues L, Kotenyova T, Flores A, Nordlund P, FEBS Lett. 2008 Oct 29;582(25-26):3590-4. Epub 2008 Sep 21. PMID:18812174
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (2vm6.pdb1.gz) 30 Kb
  • LPC: Ligand-Protein Contacts for 2VM6
  • CSU: Contacts of Structural Units for 2VM6
  • Likely Quarternary Molecular Structure file(s) for 2VM6
  • Structure Factors (80 Kb)
  • Retrieve 2VM6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VM6 from S2C, [Save to disk]
  • Re-refined 2vm6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VM6 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 2VM6
  • 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 2VM6, from MSDmotif at EBI
  • Fold representative 2vm6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vm6_A] [2vm6_B] [2vm6]
  • SWISS-PROT database: [O43521] [Q16548]
  • Belongs to the pro-apoptotic bcl-2-family protein bim (bim) family according to TCDB.
  • Domain organization of [B2L11_HUMAN] [B2LA1_HUMAN] by SWISSPFAM
  • Domain found in 2VM6: [BCL ] by SMART
  • Other resources with information on 2VM6
  • Community annotation for 2VM6 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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