2FK1 Metal Binding Protein date Jan 03, 2006
title Structure Of The Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain In 'Small Unit Cell' Form, Cu(II)-Bound
authors G.K.W.Kong, M.W.Parker
compound source
Molecule: Amyloid Beta A4 Protein Precursor
Chain: A
Fragment: Residues 133 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 21 21 21
R_factor 0.188 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
31.437 32.545 50.402 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand CU enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


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] (16 Kb) [Save to disk]
  • Biological Unit Coordinates (2fk1.pdb1.gz) 12 Kb
  • LPC: Ligand-Protein Contacts for 2FK1
  • CSU: Contacts of Structural Units for 2FK1
  • Likely Quarternary Molecular Structure file(s) for 2FK1
  • Structure Factors (52 Kb)
  • Retrieve 2FK1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2FK1 from S2C, [Save to disk]
  • Re-refined 2fk1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2FK1 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 2FK1
  • 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 2FK1, from MSDmotif at EBI
  • Fold representative 2fk1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2fk1] [2fk1_A]
  • 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 2FK1: [A4_EXTRA ] by SMART
  • Alignments of the sequence of 2FK1 with the sequences similar proteins can be viewed for 2FK1'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 2FK1
  • Community annotation for 2FK1 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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