2ZN9 Apoptosis date Apr 22, 2008
title Crystal Structure Of Ca2+-Bound Form Of Des3-20alg-2
authors H.Suzuki, M.Kawasaki, T.Inuzuka, T.Kakiuchi, H.Shibata, S.Wakatsu
compound source
Molecule: Programmed Cell Death Protein 6
Chain: A, B
Fragment: Residues 20-191
Synonym: Apoptosis-Linked Gene 2 Protein, Probable Calcium- Protein Alg-2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdcd6, Alg2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3d
symmetry Space Group: P 41
R_factor 0.234 R_Free 0.298
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.024 72.024 91.663 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 12P, 2PE, CA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • protein binding, bridging in...
  • COPII vesicle coating

  • Primary referenceStructural basis for Ca2+ -dependent formation of ALG-2/Alix peptide complex: Ca2+/EF3-driven arginine switch mechanism., Suzuki H, Kawasaki M, Inuzuka T, Okumura M, Kakiuchi T, Shibata H, Wakatsuki S, Maki M, Structure. 2008 Oct 8;16(10):1562-73. PMID:18940611
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (63 Kb) [Save to disk]
  • Biological Unit Coordinates (2zn9.pdb1.gz) 58 Kb
  • Biological Unit Coordinates (2zn9.pdb2.gz) 58 Kb
  • LPC: Ligand-Protein Contacts for 2ZN9
  • CSU: Contacts of Structural Units for 2ZN9
  • Likely Quarternary Molecular Structure file(s) for 2ZN9
  • Structure Factors (129 Kb)
  • Retrieve 2ZN9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZN9 from S2C, [Save to disk]
  • Re-refined 2zn9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ZN9 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 2ZN9
  • 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
  • 3D motif for 2ZN9, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2zn9_A] [2zn9] [2zn9_B]
  • SWISS-PROT database: [O75340]
  • Belongs to the general secretory pathway (sec) family according to TCDB.
  • Domain organization of [PDCD6_HUMAN] by SWISSPFAM
  • Domain found in 2ZN9: [EFh ] by SMART
  • Other resources with information on 2ZN9
  • Community annotation for 2ZN9 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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