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- PDB-7k1d: Crystal structure of human insulin degrading enzyme (IDE) in comp... -

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Basic information

Entry
Database: PDB / ID: 7k1d
TitleCrystal structure of human insulin degrading enzyme (IDE) in complex with compound BDM_77291
ComponentsInsulin-degrading enzyme
KeywordsHYDROLASE/HYDROLASE INHBITOR / Hydrolase / inhibitor / HYDROLASE-HYDROLASE INHBITOR complex
Function / homology
Function and homology information


insulysin / ubiquitin recycling / insulin metabolic process / insulin catabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / regulation of aerobic respiration / peptide catabolic process ...insulysin / ubiquitin recycling / insulin metabolic process / insulin catabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / regulation of aerobic respiration / peptide catabolic process / amyloid-beta clearance / peroxisomal matrix / amyloid-beta metabolic process / Insulin receptor recycling / peptide binding / proteolysis involved in protein catabolic process / Peroxisomal protein import / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / positive regulation of protein catabolic process / insulin receptor signaling pathway / peroxisome / positive regulation of protein binding / 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 / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal ...Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / 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-VQD / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 2
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)231,30214
Polymers229,1232
Non-polymers2,17912
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint31 kcal/mol
Surface area73800 Å2
Unit cell
Length a, b, c (Å)264.313, 264.313, 90.468
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

#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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-VQD / (3R)-3-{4-[(3R)-4-(3,4-difluorobenzene-1-carbonyl)morpholin-3-yl]-1H-1,2,3-triazol-1-yl}-N-hydroxy-4-(naphthalen-2-yl)butanamide


Mass: 521.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H25F2N5O4 / 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
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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
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: 3→50 Å / Num. obs: 106330 / % possible obs: 100 % / Observed criterion σ(I): 1.2 / Redundancy: 10.3 % / Biso Wilson estimate: 60.67 Å2 / CC1/2: 0.987 / CC star: 0.997 / Net I/σ(I): 10.9
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 2735 / CC1/2: 0.46 / CC star: 0.794

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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: 3→45.42 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 3004 2.83 %
Rwork0.1563 --
obs0.1574 106150 75.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15663 0 144 0 15807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116195
X-RAY DIFFRACTIONf_angle_d1.18521895
X-RAY DIFFRACTIONf_dihedral_angle_d15.9082197
X-RAY DIFFRACTIONf_chiral_restr0.0592333
X-RAY DIFFRACTIONf_plane_restr0.0072822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.050.4459650.32572347X-RAY DIFFRACTION36
3.05-3.10.3211840.31552842X-RAY DIFFRACTION43
3.1-3.160.3329880.28313062X-RAY DIFFRACTION47
3.16-3.220.3659940.27383264X-RAY DIFFRACTION50
3.22-3.290.3307970.26743307X-RAY DIFFRACTION51
3.29-3.360.29131000.25233374X-RAY DIFFRACTION51
3.36-3.440.2733960.24173430X-RAY DIFFRACTION53
3.44-3.520.22741070.20523724X-RAY DIFFRACTION57
3.52-3.620.24571140.17524121X-RAY DIFFRACTION63
3.62-3.720.22861360.15974477X-RAY DIFFRACTION69
3.72-3.840.19051480.15674983X-RAY DIFFRACTION77
3.84-3.980.2231680.15235828X-RAY DIFFRACTION89
3.98-4.140.1911890.14496295X-RAY DIFFRACTION97
4.14-4.330.17191980.1356552X-RAY DIFFRACTION99
4.33-4.560.13971880.126497X-RAY DIFFRACTION100
4.56-4.840.13961830.11636518X-RAY DIFFRACTION100
4.84-5.210.15071990.12916499X-RAY DIFFRACTION100
5.22-5.740.18251930.14796538X-RAY DIFFRACTION100
5.74-6.570.1771900.16966505X-RAY DIFFRACTION100
6.57-8.260.191900.14856518X-RAY DIFFRACTION100
8.27-45.420.16071770.12856465X-RAY DIFFRACTION99

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