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
crystal cell	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 Diffraction	resolution	2.70 Å
ligand	ACT, BU4, SO4	enzyme
Primary reference	Structure 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_B] [3ktm_C] [3ktm_D] [3ktm_E] [3ktm_F] [3ktm_G] [3ktm_H] SWISS-PROT database: Domain organization of by SWISSPFAM 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)

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