2OTK De Novo Protein, Peptide Binding Protein date Feb 08, 2007
title Structure Of Alzheimer Ab Peptide In Complex With An Engineered Binding Protein
authors W.Hoyer, T.Hard
compound source
Molecule: Amyloid Beta A4 Protein
Chain: C
Fragment: Residues 672-711
Synonym: Igg-Binding Protein A, Staphylococcal Protein A
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Zab3 Affibody Dimer
Chain: E, F
Engineered: Yes
Organism_scientific: Engineered Binding Protein
Expression_system: Escherichia Coli
Expression_system_taxid: 562
methodSolution NMR
Primary referenceStabilization of a beta-hairpin in monomeric Alzheimer's amyloid-beta peptide inhibits amyloid formation., Hoyer W, Gronwall C, Jonsson A, Stahl S, Hard T, Proc Natl Acad Sci U S A. 2008 Apr 1;105(13):5099-104. Epub 2008 Mar 28. PMID:18375754
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (665 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 2OTK
  • Original NMR restraints for 2OTK from PDB
  • Retrieve 2OTK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OTK from S2C, [Save to disk]
    • View 2OTK 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 2OTK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2OTK, from MSDmotif at EBI
  • Fold representative 2otk from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2otk_C] [2otk_E] [2otk_F]
  • SWISS-PROT database: [P05067]
  • Belongs to the amyloid -protein peptide (app) family according to TCDB.
  • Domain organization of [A4_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2OTK with the sequences similar proteins can be viewed for 2OTK's classification [A4_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 [A4_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 2OTK
  • Community annotation for 2OTK 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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