3KTM Cell Adhesion, Signaling Protein date Nov 25, 2009
title Structure Of The Heparin-Induced E1-Dimer Of The Amyloid Pre Protein (App)
authors S.O.Dahms, S.Hoefgen, D.Roeser, B.Schlott, K.H.Guhrs, M.E.Than
compound source
Molecule: Amyloid Beta A4 Protein
Chain: A, B, C, D, E, F, G, H
Fragment: Unp Residues 18-190
Synonym: Alzheimer Disease Amyloid Protein, Abpp, App
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: Origami B(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: H 3
R_factor 0.215 R_Free 0.250
length a length b length c angle alpha angle beta angle gamma
143.990 143.990 351.190 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand ACT, BU4, SO4 enzyme
F, A, E, B, H, C, D, G

Primary referenceStructure and biochemical analysis of the heparin-induced E1 dimer of the amyloid precursor protein., Dahms SO, Hoefgen S, Roeser D, Schlott B, Guhrs KH, Than ME, Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5381-6. Epub 2010 Mar 8. PMID:20212142
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (241 Kb) [Save to disk]
  • Biological Unit Coordinates (3ktm.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (3ktm.pdb2.gz) 61 Kb
  • Biological Unit Coordinates (3ktm.pdb3.gz) 62 Kb
  • Biological Unit Coordinates (3ktm.pdb4.gz) 61 Kb
  • Biological Unit Coordinates (3ktm.pdb5.gz) 33 Kb
  • Biological Unit Coordinates (3ktm.pdb6.gz) 32 Kb
  • Biological Unit Coordinates (3ktm.pdb7.gz) 33 Kb
  • Biological Unit Coordinates (3ktm.pdb8.gz) 33 Kb
  • Biological Unit Coordinates (3ktm.pdb9.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 3KTM
  • CSU: Contacts of Structural Units for 3KTM
  • Structure Factors (606 Kb)
  • Retrieve 3KTM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KTM from S2C, [Save to disk]
  • Re-refined 3ktm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KTM 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 3KTM
  • 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 3KTM, from MSDmotif at EBI
  • Fold representative 3ktm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ktm_A] [3ktm] [3ktm_D] [3ktm_H] [3ktm_G] [3ktm_F] [3ktm_B] [3ktm_C] [3ktm_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3KTM: [A4_EXTRA ] by SMART
  • Alignments of the sequence of 3KTM with the sequences similar proteins can be viewed for 3KTM's classification 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 at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3KTM
  • Community annotation for 3KTM 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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