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Yorodumi- PDB-4pes: Crystal structure of insulin degrading enzyme complexed with inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pes | |||||||||
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Title | Crystal structure of insulin degrading enzyme complexed with inhibitor tert-butyl [(2S)-2-(2,5-difluorophenyl)-3-(quinolin-3-yl)propyl]carbamate | |||||||||
Components |
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Keywords | HYDROLASE/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 / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | |||||||||
Authors | Wang, Y. / Guo, S. | |||||||||
Citation | Journal: To Be Published Title: Crystal structure of IDE complexed with an inhibitor Authors: Durham, T.B. / Toth, J.L. / Klimkowski, V.J. / Cao, J.X.C. / Siesky, A.M. / Alexander-Chacko, J. / Wu, G.Y. / Dixon, J.T. / McGee, J.E. / Wang, Y. / Guo, S. / Cavitt, R.N. / Schindler, J. / ...Authors: Durham, T.B. / Toth, J.L. / Klimkowski, V.J. / Cao, J.X.C. / Siesky, A.M. / Alexander-Chacko, J. / Wu, G.Y. / Dixon, J.T. / McGee, J.E. / Wang, Y. / Guo, S. / Cavitt, R.N. / Schindler, J. / Thibodeaux, S.J. / Calvert, N.A. / Coghlan, M.J. / Sindelar, D.K. / Christe, M. / Kiselyov, V.V. / Dodson, M. / Sloop, K.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pes.cif.gz | 414.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pes.ent.gz | 327.5 KB | Display | PDB format |
PDBx/mmJSON format | 4pes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/4pes ftp://data.pdbj.org/pub/pdb/validation_reports/pe/4pes | HTTPS FTP |
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-Related structure data
Related structure data | 2g47S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 44 - 1012 / Label seq-ID: 14 - 982
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-Components
#1: Protein | Mass: 114493.484 Da / Num. of mol.: 2 / Fragment: UNP residues 42-1019 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P14735, insulysin #2: Protein/peptide | Mass: 231.249 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2 mM sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 12, 2011 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→122.69 Å / Num. obs: 119894 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rsym value: 0.07 / Net I/σ(I): 7.9 |
Reflection shell | Highest resolution: 2.2 Å / Rsym value: 0.606 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2G47 Resolution: 2.21→122.69 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.065 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.756 Å2
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Refinement step | Cycle: 1 / Resolution: 2.21→122.69 Å
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Refine LS restraints |
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