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- PDB-4gs8: Structure analysis of cysteine free insulin degrading enzyme (ide... -

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Basic information

Entry
Database: PDB / ID: 4gs8
TitleStructure analysis of cysteine free insulin degrading enzyme (ide) with compound bdm43079 [{[(s)-2-(1h-imidazol-4-yl)-1-methylcarbamoyl-ethylcarbamoyl]-methyl}-(3-phenyl-propyl)-amino]-acetic acid
ComponentsInsulin-degrading enzyme
KeywordsHYDROLASE/HYDROLASE INHIBITOR / INSULIN DEGRADING ENZYME / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


insulysin / beta-endorphin binding / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / cytosolic proteasome complex / insulin binding ...insulysin / beta-endorphin binding / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / cytosolic proteasome complex / insulin binding / regulation of aerobic respiration / peptide catabolic process / amyloid-beta clearance / peroxisomal matrix / amyloid-beta metabolic process / positive regulation of protein binding / Insulin receptor recycling / negative regulation of proteolysis / 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 / amyloid-beta binding / virus receptor activity / endopeptidase activity / basolateral plasma membrane / Ub-specific processing proteases / external side of plasma membrane / protein-containing complex binding / cell surface / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / 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, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / 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
Chem-MGJ / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsGuo, Q. / Deprez-Poulain, R. / Deprez, B. / Tang, W.J.
CitationJournal: Eur.J.Med.Chem. / Year: 2014
Title: Imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, substrate-dependent modulators of insulin-degrading enzyme in amyloid-beta hydrolysis.
Authors: Charton, J. / Gauriot, M. / Guo, Q. / Hennuyer, N. / Marechal, X. / Dumont, J. / Hamdane, M. / Pottiez, V. / Landry, V. / Sperandio, O. / Flipo, M. / Buee, L. / Staels, B. / Leroux, F. / ...Authors: Charton, J. / Gauriot, M. / Guo, Q. / Hennuyer, N. / Marechal, X. / Dumont, J. / Hamdane, M. / Pottiez, V. / Landry, V. / Sperandio, O. / Flipo, M. / Buee, L. / Staels, B. / Leroux, F. / Tang, W.J. / Deprez, B. / Deprez-Poulain, R.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)230,0556
Polymers229,1212
Non-polymers9344
Water1,36976
1
A: Insulin-degrading enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0273
Polymers114,5611
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Insulin-degrading enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0273
Polymers114,5611
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)263.553, 263.553, 91.095
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 / Fragment: UNP RESIDUES 42-1019
Mutation: C110L,E111Q,C171S,C178A,C257V,C414L,C573N,C590S,C789SC812A,C819A,C904S,C966N,C974A
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-MGJ / N-(carboxymethyl)-N-(3-phenylpropyl)glycyl-N-methyl-L-histidinamide / [{[(S)-2-(1H-Imidazol-4-yl)-1-methylcarbamoyl-ethylcarbamoyl]-methyl}-(3-phenyl-propyl)-amino]-acetic acid


Mass: 401.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H27N5O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.99 Å3/Da / Density % sol: 69.14 %
Crystal growMethod: 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 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9597
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 28, 2010
RadiationMonochromator: MAR 345 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9597 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 69469 / % possible obs: 100 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.99→50 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CWW

3cww


Resolution: 2.99→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.478 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.837 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3679 5 %RANDOM
Rwork0.178 ---
obs0.181 69469 99.8 %-
all-69469 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.55 Å20 Å2
2--1.09 Å2-0 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.99→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15590 0 60 76 15726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02216040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.96921696
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44551904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97124.509794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.717152862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1791582
X-RAY DIFFRACTIONr_chiral_restr0.120.22330
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112226
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6811.59552
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.415215460
X-RAY DIFFRACTIONr_scbond_it2.35536488
X-RAY DIFFRACTIONr_scangle_it4.174.56236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.99→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 269 -
Rwork0.263 5051 -
obs--99.22 %

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