2WK3	Hydrolase	date	Jun 05, 2009
title	Crystal Structure Of Human Insulin-Degrading Enzyme In Complex With Amyloid-Beta (1-42)
authors	Q.Guo, W.J.Tang
compound		source
Molecule: Insulin Degrading Enzyme Chain: A, B Synonym: Insulin Protease, Insulysin, Insulinase Ec: 3.4.24.56 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector: Pex
Molecule: Beta-Amyloid Protein 42 Chain: C, D Fragment: Beta-Amyloid Protein 42, Residues 672-713 Synonym: Beta-App42, Amyloid Beta A4 Protein Synonym: Amyloid Beta, Alzheimer Disease Amyloid Protein, Abpp, Appi, App, Prea4, Cerebral Vascular Amyloid Peptide, Cvap, Protease Nexin-II, Pn-II Synonym: App, Abpp, Alzheimer'S Disease Amyloid Protein, Cerebral Vascular Amyloid Peptide, Cvap, Protease Nexin-II, Pn-II, Appi; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Bl21(De3) Expression_system_strain: Bl21(De3)
symmetry	Space Group: P 65	R_factor 0.187 R_Free 0.232
crystal cell	length a length b length c angle alpha angle beta angle gamma 261.628 261.628 90.675 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.59 Å
ligand	ZN	enzyme	Hydrolase E.C.3.4.24.56 BRENDA
Gene Ontology	Chain Function Process Component A, B nucleotide binding beta-amyloid binding glycoprotein binding catalytic activity metalloendopeptidase activit... receptor binding protein binding ATP binding peptidase activity metallopeptidase activity zinc ion binding hydrolase activity ATPase activity peptide hormone binding beta-endorphin binding peptide binding protein homodimerization act... ubiquitin binding insulin binding metal ion binding ATP catabolic process proteolysis metabolic process insulin receptor signaling p... determination of adult lifes... bradykinin catabolic process... ubiquitin homeostasis virus-host interaction positive regulation of prote... hormone catabolic process cellular protein catabolic p... negative regulation of prote... beta-amyloid metabolic proce... protein homooligomerization protein homotetramerization protein heterooligomerizatio... proteolysis involved in cell... insulin metabolic process insulin catabolic process extracellular region extracellular space nucleus cytoplasm mitochondrion peroxisome peroxisomal matrix cytosol plasma membrane cell surface membrane cytosolic proteasome complex...
Primary reference	Molecular Basis for the Recognition and Cleavages of IGF-II, TGF-alpha, and Amylin by Human Insulin-Degrading Enzyme., Guo Q, Manolopoulou M, Bian Y, Schilling AB, Tang WJ, J Mol Biol. 2009 Nov 5. PMID:19896952

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (329 Kb) [Save to disk] Biological Unit Coordinates (2wk3.pdb1.gz) 162 Kb Biological Unit Coordinates (2wk3.pdb2.gz) 163 Kb LPC: Ligand-Protein Contacts for 2WK3 CSU: Contacts of Structural Units for 2WK3 Structure Factors (1583 Kb) Retrieve 2WK3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2WK3 from S2C, [Save to disk] Re-refined 2wk3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2WK3 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 2WK3

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 2WK3, from MSDmotif at EBI Fold representative 2wk3 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2wk3_A] [2wk3_B] [2wk3_C] [2wk3_D] SWISS-PROT database: [P05067] [P14735] Belongs to the amyloid -protein peptide (app) family according to TCDB. Domain organization of [A4_HUMAN] [IDE_HUMAN] by SWISSPFAM Alignments of the sequence of 2WK3 with the sequences similar proteins can be viewed for 2WK3's classification [A4_HUMAN] [IDE_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] [IDE_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2WK3

Community annotation for 2WK3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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