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- PDB-7k1e: Crystal structure of human insulin degrading enzyme (IDE) in comp... -

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Basic information

Entry
Database: PDB / ID: 7k1e
TitleCrystal structure of human insulin degrading enzyme (IDE) in complex with compound BDM_88646
ComponentsInsulin-degrading enzyme
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / ubiquitin-modified protein reader activity / insulin binding / regulation of aerobic respiration ...insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / ubiquitin-modified protein reader activity / insulin binding / regulation of aerobic respiration / peptide catabolic process / amyloid-beta clearance / peroxisomal matrix / amyloid-beta metabolic process / Insulin receptor recycling / proteolysis involved in protein catabolic process / Peroxisomal protein import / peptide binding / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / positive regulation of protein catabolic process / peroxisome / positive regulation of protein binding / insulin receptor signaling pathway / virus receptor activity / basolateral plasma membrane / endopeptidase activity / Ub-specific processing proteases / external side of plasma membrane / cell surface / protein homodimerization activity / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular exosome / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Chem-VQG / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiang, W.G. / Deprez, R. / Bosc, D. / Tang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01 GM121964 United States
CitationJournal: To Be Published
Title: Crystal structure of human insulin degrading enzyme (IDE) in complex with compound 3
Authors: Liang, W.G. / Deprez, R. / Bosc, D. / Tang, W.
History
DepositionSep 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin-degrading enzyme
B: Insulin-degrading enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,22614
Polymers229,1232
Non-polymers2,10312
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint33 kcal/mol
Surface area74800 Å2
Unit cell
Length a, b, c (Å)267.880, 267.880, 89.611
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Insulin-degrading enzyme / Abeta-degrading protease / Insulin protease / Insulinase / Insulysin


Mass: 114561.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDE
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P14735, insulysin

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Non-polymers , 5 types, 231 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-VQG / 3,4-difluoro-N-[(1S)-1-{1-[(2R)-4-(hydroxyamino)-4-oxo-1-(5,6,7,8-tetrahydronaphthalen-2-yl)butan-2-yl]-1H-1,2,3-triazol-4-yl}ethyl]benzamide


Mass: 483.510 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27F2N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8O2
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.57 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 5000, 100mM HEPES, 14% Tacsimate, 10% Dioxane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 90366 / % possible obs: 100 % / Redundancy: 20.5 % / Biso Wilson estimate: 47.3 Å2 / CC1/2: 0.995 / Net I/σ(I): 15.7
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 4495 / CC1/2: 0.616

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IFH

4ifh


Resolution: 2.8→43.84 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 2010 2.25 %
Rwork0.1581 --
obs0.1592 89309 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15677 0 138 219 16034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01316210
X-RAY DIFFRACTIONf_angle_d1.47721917
X-RAY DIFFRACTIONf_dihedral_angle_d14.5642197
X-RAY DIFFRACTIONf_chiral_restr0.0672336
X-RAY DIFFRACTIONf_plane_restr0.0092828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.32071230.26225241X-RAY DIFFRACTION84
2.87-2.950.32281420.23856127X-RAY DIFFRACTION98
2.95-3.030.29011410.23346272X-RAY DIFFRACTION100
3.03-3.130.2811430.21936286X-RAY DIFFRACTION100
3.13-3.240.29921460.21316295X-RAY DIFFRACTION100
3.24-3.370.2441450.18276266X-RAY DIFFRACTION100
3.37-3.530.22981460.16926345X-RAY DIFFRACTION100
3.53-3.710.23441450.15776293X-RAY DIFFRACTION100
3.71-3.950.21091430.14816296X-RAY DIFFRACTION100
3.95-4.250.19181470.13416329X-RAY DIFFRACTION100
4.25-4.680.16251450.11586318X-RAY DIFFRACTION100
4.68-5.350.15151460.12066347X-RAY DIFFRACTION100
5.35-6.740.18661480.15476387X-RAY DIFFRACTION100
6.74-43.840.14761500.12846497X-RAY DIFFRACTION100

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