3D8D Protein Binding date May 23, 2008
title Crystal Structure Of The Human Fe65-Ptb1 Domain
authors J.Radzimanowski, S.Ravaud, I.Sinning, K.Wild
compound source
Molecule: Amyloid Beta A4 Precursor Protein-Binding Family 1;
Chain: A, B
Fragment: Fe65-Ptb1 Domain
Synonym: Fe65-Ptb1, Fe65 Protein
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)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24d
symmetry Space Group: P 21 21 21
R_factor 0.202 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.756 79.574 83.974 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand EDO, HG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of the human Fe65-PTB1 domain., Radzimanowski J, Ravaud S, Schlesinger S, Koch J, Beyreuther K, Sinning I, Wild K, J Biol Chem. 2008 Aug 22;283(34):23113-20. Epub 2008 Jun 11. PMID:18550529
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (3d8d.pdb1.gz) 25 Kb
  • Biological Unit Coordinates (3d8d.pdb2.gz) 25 Kb
  • Biological Unit Coordinates (3d8d.pdb3.gz) 48 Kb
  • Biological Unit Coordinates (3d8d.pdb4.gz) 48 Kb
  • Biological Unit Coordinates (3d8d.pdb5.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 3D8D
  • CSU: Contacts of Structural Units for 3D8D
  • Likely Quarternary Molecular Structure file(s) for 3D8D
  • Structure Factors (227 Kb)
  • Retrieve 3D8D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D8D from S2C, [Save to disk]
  • Re-refined 3d8d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D8D 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 3D8D
  • 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 3D8D, from MSDmotif at EBI
  • Fold representative 3d8d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d8d_B] [3d8d] [3d8d_A]
  • SWISS-PROT database: [O00213]
  • Domain organization of [APBB1_HUMAN] by SWISSPFAM
  • Domain found in 3D8D: [PTB ] by SMART
  • Other resources with information on 3D8D
  • Community annotation for 3D8D 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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