2G56 Hydrolase date Feb 22, 2006
title Crystal Structure Of Human Insulin-Degrading Enzyme In Complex With Insulin B Chain
authors Y.Shen, W.J.Tang
compound source
Molecule: Insulin-Degrading Enzyme
Chain: A, B
Synonym: Insulysin, Insulinase, Insulin Protease
Ec: 3.4.24.56
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ide
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pproex

Molecule: Insulin
Chain: C, D
Fragment: Insulin B Chain, Residues 25-54
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Homo Sapiens (Humans)
symmetry Space Group: P 65
R_factor 0.205 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
262.250 262.250 90.610 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand DIO enzyme Hydrolase E.C.3.4.24.56 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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...
  • D, C
  • protease binding
  • insulin receptor binding
  • insulin-like growth factor r...
  • hormone activity
  • protein binding
  • MAPK cascade
  • negative regulation of acute...
  • carbohydrate metabolic proce...
  • glucose metabolic process
  • energy reserve metabolic pro...
  • regulation of transcription,...
  • regulation of cellular amino...
  • acute-phase response
  • G-protein coupled receptor s...
  • cell-cell signaling
  • positive regulation of cell ...
  • insulin receptor signaling p...
  • positive regulation of phosp...
  • glucose transport
  • regulation of transmembrane ...
  • positive regulation of cell ...
  • positive regulation of cell ...
  • endocrine pancreas developme...
  • positive regulation of prote...
  • activation of protein kinase...
  • positive regulation of cellu...
  • negative regulation of prote...
  • regulation of protein locali...
  • negative regulation of NAD(P...
  • wound healing
  • negative regulation of prote...
  • glucose homeostasis
  • negative regulation of apopt...
  • positive regulation of MAPK ...
  • cellular protein metabolic p...
  • small molecule metabolic pro...
  • positive regulation of nitri...
  • positive regulation of cell ...
  • negative regulation of gluco...
  • positive regulation of glyco...
  • positive regulation of DNA r...
  • negative regulation of glyco...
  • positive regulation of glyco...
  • positive regulation of mitos...
  • negative regulation of prote...
  • negative regulation of vasod...
  • positive regulation of vasod...
  • negative regulation of fatty...
  • positive regulation of gluco...
  • positive regulation of insul...
  • alpha-beta T cell activation...
  • positive regulation of lipid...
  • regulation of protein secret...
  • negative regulation of prote...
  • positive regulation of cytok...
  • positive regulation of pepti...
  • regulation of insulin secret...
  • negative regulation of lipid...
  • positive regulation of nitri...
  • positive regulation of NF-ka...
  • positive regulation of prote...
  • fatty acid homeostasis
  • negative regulation of respi...
  • positive regulation of respi...
  • positive regulation of pepti...
  • positive regulation of brown...
  • negative regulation of feedi...
  • extracellular region
  • extracellular space
  • endoplasmic reticulum lumen
  • Golgi lumen
  • endosome lumen
  • secretory granule lumen
  • Primary referenceStructures of human insulin-degrading enzyme reveal a new substrate recognition mechanism., Shen Y, Joachimiak A, Rosner MR, Tang WJ, Nature. 2006 Oct 19;443(7113):870-4. Epub 2006 Oct 11. PMID:17051221
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (346 Kb) [Save to disk]
  • Biological Unit Coordinates (2g56.pdb1.gz) 172 Kb
  • Biological Unit Coordinates (2g56.pdb2.gz) 173 Kb
  • LPC: Ligand-Protein Contacts for 2G56
  • CSU: Contacts of Structural Units for 2G56
  • Likely Quarternary Molecular Structure file(s) for 2G56
  • Structure Factors (2160 Kb)
  • Retrieve 2G56 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2G56 from S2C, [Save to disk]
  • Re-refined 2g56 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2G56 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).
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  • Visual 3D analysis of 2G56
  • 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 2G56, from MSDmotif at EBI
  • Fold representative 2g56 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2g56_A] [2g56_B] [2g56_C] [2g56_D]
  • SWISS-PROT database: [P14735] [P01308]
  • Domain organization of [IDE_HUMAN] [INS_HUMAN] by SWISSPFAM
  • Domain found in 2G56: [IlGF ] by SMART
  • Alignments of the sequence of 2G56 with the sequences similar proteins can be viewed for 2G56's classification [IDE_HUMAN] [INS_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 [IDE_HUMAN] [INS_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2G56
  • Community annotation for 2G56 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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