3DXC Protein Binding date Jul 24, 2008
title Crystal Structure Of The Intracellular Domain Of Human App In Complex With Fe65-Ptb2
authors J.Radzimanowski, I.Sinning, K.Wild
compound source
Molecule: Amyloid Beta A4 Protein-Binding Family B Member 1;
Chain: A, C
Fragment: Ptb2 Domain, Unp Residues 534-667
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apbb1, Fe65, Rir
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21d

Molecule: Amyloid Beta A4 Protein
Chain: B, D
Fragment: App Intracellular Domain, Unp Residues 739-770
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: App, A4, Ad1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pettrx_1b
symmetry Space Group: P 61
R_factor 0.202 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
114.320 114.320 74.850 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
Primary referenceStructure of the intracellular domain of the amyloid precursor protein in complex with Fe65-PTB2., Radzimanowski J, Simon B, Sattler M, Beyreuther K, Sinning I, Wild K, EMBO Rep. 2008 Nov;9(11):1134-40. Epub 2008 Oct 3. PMID:18833287
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (3dxc.pdb1.gz) 29 Kb
  • Biological Unit Coordinates (3dxc.pdb2.gz) 28 Kb
  • CSU: Contacts of Structural Units for 3DXC
  • Likely Quarternary Molecular Structure file(s) for 3DXC
  • Structure Factors (310 Kb)
  • Retrieve 3DXC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DXC from S2C, [Save to disk]
  • Re-refined 3dxc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DXC 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 3DXC
  • 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 3DXC, from MSDmotif at EBI
  • Fold representative 3dxc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dxc_D] [3dxc_B] [3dxc_A] [3dxc] [3dxc_C]
  • SWISS-PROT database: [P05067] [O00213]
  • Belongs to the amyloid -protein peptide (app) family according to TCDB.
  • Domain organization of [A4_HUMAN] [APBB1_HUMAN] by SWISSPFAM
  • Domain found in 3DXC: [PTB ] by SMART
  • Other resources with information on 3DXC
  • Community annotation for 3DXC 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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