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- PDB-3cww: Crystal Structure of IDE-bradykinin complex -

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Basic information

Entry
Database: PDB / ID: 3cww
TitleCrystal Structure of IDE-bradykinin complex
Components
  • Insulin-degrading enzyme
  • bradykinin N-terminal tetrapeptide analogue
KeywordsHYDROLASE / A-beta degrading enzyme / criptidase / bradykinin / kinins
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 / metalloendopeptidase activity / antigen processing and presentation of endogenous peptide antigen via MHC class I / peroxisome / positive regulation of protein catabolic process / virus receptor activity / insulin receptor signaling pathway / positive regulation of protein binding / 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 / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / 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) ...Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 1,4-DIETHYLENE DIOXIDE / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.96 Å
AuthorsMalito, E. / Tang, W.J.
CitationJournal: Biochemistry / Year: 2008
Title: Molecular Bases for the Recognition of Short Peptide Substrates and Cysteine-Directed Modifications of Human Insulin-Degrading Enzyme
Authors: Malito, E. / Ralat, L.A. / Manolopoulou, M. / Tsay, J.L. / Wadlington, N.L. / Tang, W.J.
History
DepositionApr 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Insulin-degrading enzyme
B: Insulin-degrading enzyme
D: bradykinin N-terminal tetrapeptide analogue
E: bradykinin N-terminal tetrapeptide analogue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,30415
Polymers228,4974
Non-polymers80811
Water30,6071699
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-61 kcal/mol
Surface area72470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)262.448, 262.448, 90.628
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABDE

#1: Protein Insulin-degrading enzyme / / E.C.3.4.24.56 / Insulysin / Insulinase / Insulin protease


Mass: 113893.922 Da / Num. of mol.: 2
Mutation: C110L, E111Q, C171S, C178A, C257V, C414L, C573N, C590S, C789S, C812A, C819A, C904S, C966N, C974A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDE, RP11-366I13.1-001, hCG_1810909 / Plasmid: pProEX-CF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P14735, insulysin
#2: Protein/peptide bradykinin N-terminal tetrapeptide analogue


Mass: 354.400 Da / Num. of mol.: 2 / Fragment: N-terminal bradykinin
Source method: isolated from a genetically manipulated source

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Non-polymers , 4 types, 1710 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H8O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1699 / Source method: isolated from a natural source / Formula: H2O

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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: 3.94 Å3/Da / Density % sol: 68.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 13% PEGMME 5000, 100mM HEPES, pH 7.0, 10%, Tacsimate, 10% dioxane, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 248865 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 28.08 Å2 / Rsym value: 0.088 / Net I/σ(I): 15.7
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.75 / Num. unique all: 23609 / Rsym value: 0.501 / % possible all: 93.1

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementStarting model: 2JG4
Resolution: 1.96→29.77 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 12495 5.03 %random
Rwork0.181 ---
obs0.183 248597 97.64 %-
all-248597 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 13.72 Å2 / Biso mean: 30.48 Å2 / Biso min: 85.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.118 Å20 Å20 Å2
2---0.118 Å2-0 Å2
3---0.236 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15534 0 48 1699 17281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115968
X-RAY DIFFRACTIONf_angle_deg1.13621597
X-RAY DIFFRACTIONf_chiral_restr0.0782326
X-RAY DIFFRACTIONf_plane_restr0.0052791
X-RAY DIFFRACTIONf_dihedral_angle_d16.3255933
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-1.9820.2983460.2556893723986
1.982-2.0060.2664000.2447720812096
2.006-2.030.2564120.237881829398
2.03-2.0560.2624240.2337958838299
2.056-2.0830.2584080.2187908831699
2.083-2.1110.254150.2167982839799
2.111-2.1410.2514130.21279548367100
2.141-2.1730.2354780.2017900837899
2.173-2.2070.2363970.280468443100
2.207-2.2440.2544120.2017932834499
2.244-2.2820.2464420.1917972841499
2.282-2.3240.2224580.18979988456100
2.324-2.3680.2274310.18979668397100
2.368-2.4170.2234020.18780218423100
2.417-2.4690.2254370.18279788415100
2.469-2.5270.2364300.1878021845199
2.527-2.590.2334030.1788037844099
2.59-2.660.2024070.1758002840999
2.66-2.7380.23970.1738010840799
2.738-2.8260.2194300.1768007843799
2.826-2.9270.2044190.1777966838599
2.927-3.0440.194070.1667937834499
3.044-3.1830.1854220.1617899832198
3.183-3.350.1814370.1657938837598
3.35-3.560.1834420.1647860830298
3.56-3.8340.1843940.167870826497
3.834-4.2190.1854380.1617833827197
4.219-4.8270.1753670.1577818818596
4.827-6.0740.2054060.1937638804494
6.074-29.7730.2034210.1997157757886

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