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- PDB-4qia: Crystal structure of human insulin degrading enzyme (ide) in comp... -

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Basic information

Entry
Database: PDB / ID: 4qia
TitleCrystal structure of human insulin degrading enzyme (ide) in complex with inhibitor N-benzyl-N-(carboxymethyl)glycyl-L-histidine
ComponentsInsulin-degrading enzyme
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / inhibitor:41371
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 / 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
N-benzyl-N-(carboxymethyl)glycyl-L-histidine / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.202 Å
AuthorsGuo, Q. / Deprez-Poulain, R. / Deprez, B. / Tang, W.J.
CitationJournal: Eur.J.Med.Chem. / Year: 2015
Title: Structure-activity relationships of imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, dual binders of human insulin-degrading enzyme.
Authors: Charton, J. / Gauriot, M. / Totobenazara, J. / Hennuyer, N. / Dumont, J. / Bosc, D. / Marechal, X. / Elbakali, J. / Herledan, A. / Wen, X. / Ronco, C. / Gras-Masse, H. / Heninot, A. / ...Authors: Charton, J. / Gauriot, M. / Totobenazara, J. / Hennuyer, N. / Dumont, J. / Bosc, D. / Marechal, X. / Elbakali, J. / Herledan, A. / Wen, X. / Ronco, C. / Gras-Masse, H. / Heninot, A. / Pottiez, V. / Landry, V. / Staels, B. / Liang, W.G. / Leroux, F. / Tang, W.J. / Deprez, B. / Deprez-Poulain, R.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,9736
Polymers229,1212
Non-polymers8524
Water00
1
A: Insulin-degrading enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9863
Polymers114,5611
Non-polymers4262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Insulin-degrading enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9863
Polymers114,5611
Non-polymers4262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)264.505, 264.505, 90.543
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 114560.578 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 (E. coli) / References: UniProt: P14735, insulysin
#2: Chemical ChemComp-33K / N-benzyl-N-(carboxymethyl)glycyl-L-histidine


Mass: 360.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N4O5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.99 Å3/Da / Density % sol: 69.18 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-13% PEG MME 5000, 100 MM HEPES PH 7.0, 4-14% TACSIMATE, 10% DIOXANE, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 59616 / Num. obs: 56516 / % possible obs: 94.8 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.202→45.451 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1999 3.54 %
Rwork0.1788 --
obs0.1803 56451 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.202→45.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15582 0 48 0 15630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416017
X-RAY DIFFRACTIONf_angle_d0.81921663
X-RAY DIFFRACTIONf_dihedral_angle_d14.8926064
X-RAY DIFFRACTIONf_chiral_restr0.0322324
X-RAY DIFFRACTIONf_plane_restr0.0042809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2016-3.28170.37611360.27273655X-RAY DIFFRACTION89
3.2817-3.37040.29321480.24043944X-RAY DIFFRACTION96
3.3704-3.46950.27941400.22463930X-RAY DIFFRACTION96
3.4695-3.58150.29251490.20873915X-RAY DIFFRACTION96
3.5815-3.70940.22761480.19553897X-RAY DIFFRACTION96
3.7094-3.85790.26561460.19053942X-RAY DIFFRACTION96
3.8579-4.03330.26391410.18863923X-RAY DIFFRACTION95
4.0333-4.24580.23041390.17383901X-RAY DIFFRACTION95
4.2458-4.51160.2051370.16043917X-RAY DIFFRACTION94
4.5116-4.85960.17511430.1453851X-RAY DIFFRACTION94
4.8596-5.3480.19991430.15563884X-RAY DIFFRACTION94
5.348-6.12020.22041390.18393897X-RAY DIFFRACTION94
6.1202-7.70470.20241430.17713905X-RAY DIFFRACTION94
7.7047-45.45550.14441470.14413891X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 72.8403 Å / Origin y: -78.6871 Å / Origin z: 35.3371 Å
111213212223313233
T0.4227 Å2-0.0308 Å2-0.0396 Å2-0.4513 Å2-0.0635 Å2--0.3497 Å2
L0.4162 °20.1961 °2-0.2885 °2-0.1988 °2-0.2181 °2--0.1827 °2
S0.0133 Å °0.0141 Å °0.0279 Å °0.0296 Å °-0.0002 Å °0.0116 Å °-0.0103 Å °-0.0717 Å °-0.0102 Å °
Refinement TLS groupSelection details: all

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