2FKL Metal Binding Protein date Jan 04, 2006
title Structure Of The Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain (Residues 126- 189 Of App)
authors G.K.W.Kong, M.W.Parker
compound source
Molecule: Amyloid Beta A4 Protein Precursor
Chain: A, B
Fragment: Residues 124 To 189
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: App
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_strain: Gs115
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppic-9
symmetry Space Group: P 1 21 1
R_factor 0.222 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.694 34.823 50.810 90.00 98.53 90.00
method X-Ray Diffractionresolution 2.50 Å
Primary referenceStructural Studies of the Alzheimer's Amyloid Precursor Protein Copper-binding Domain Reveal How it Binds Copper Ions., Kong GK, Adams JJ, Harris HH, Boas JF, Curtain CC, Galatis D, Masters CL, Barnham KJ, McKinstry WJ, Cappai R, Parker MW, J Mol Biol. 2007 Mar 16;367(1):148-61. Epub 2006 Dec 21. PMID:17239395
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (26 Kb) [Save to disk]
  • Biological Unit Coordinates (2fkl.pdb1.gz) 11 Kb
  • Biological Unit Coordinates (2fkl.pdb2.gz) 12 Kb
  • CSU: Contacts of Structural Units for 2FKL
  • Likely Quarternary Molecular Structure file(s) for 2FKL
  • Structure Factors (36 Kb)
  • Retrieve 2FKL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2FKL from S2C, [Save to disk]
  • Re-refined 2fkl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2FKL 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 2FKL
  • 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 2FKL, from MSDmotif at EBI
  • Fold representative 2fkl from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2fkl_A] [2fkl_B]
  • SWISS-PROT database: [P05067]
  • Belongs to the amyloid -protein peptide (app) family according to TCDB.
  • Domain organization of [A4_HUMAN] by SWISSPFAM
  • Domain found in 2FKL: [A4_EXTRA ] by SMART
  • Alignments of the sequence of 2FKL with the sequences similar proteins can be viewed for 2FKL'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 2FKL
  • Community annotation for 2FKL at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2010
    Bioinformatics Unit
    Weizmann Institute of Science