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Yorodumi- PDB-8cgw: Insulin-regulated aminopeptidase (IRAP) in complex with an allost... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cgw | ||||||
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Title | Insulin-regulated aminopeptidase (IRAP) in complex with an allosteric benzopyran-based inhibitor | ||||||
Components | Leucyl-cystinyl aminopeptidase, pregnancy serum form | ||||||
Keywords | HYDROLASE / insulin-regulated aminopeptidase / allosteric inhibitor / benzopyran scaffold / antigen presentation / HFI-419 | ||||||
Function / homology | Function and homology information cystinyl aminopeptidase / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / negative regulation of cold-induced thermogenesis / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / early endosome lumen / Translocation of SLC2A4 (GLUT4) to the plasma membrane / female pregnancy / Endosomal/Vacuolar pathway ...cystinyl aminopeptidase / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / negative regulation of cold-induced thermogenesis / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / early endosome lumen / Translocation of SLC2A4 (GLUT4) to the plasma membrane / female pregnancy / Endosomal/Vacuolar pathway / peptide binding / protein catabolic process / cytoplasmic vesicle membrane / regulation of blood pressure / protein polyubiquitination / metallopeptidase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell-cell signaling / lysosomal membrane / perinuclear region of cytoplasm / signal transduction / proteolysis / extracellular space / zinc ion binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å | ||||||
Authors | Mpakali, A. / Stratikos, E. / Giastas, P. | ||||||
Funding support | European Union, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2024 Title: Mechanisms of Allosteric Inhibition of Insulin-Regulated Aminopeptidase. Authors: Mpakali, A. / Barla, I. / Lu, L. / Ramesh, K.M. / Thomaidis, N. / Stern, L.J. / Giastas, P. / Stratikos, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cgw.cif.gz | 885.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cgw.ent.gz | 615 KB | Display | PDB format |
PDBx/mmJSON format | 8cgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cgw_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 8cgw_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 8cgw_validation.xml.gz | 62.8 KB | Display | |
Data in CIF | 8cgw_validation.cif.gz | 85.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/8cgw ftp://data.pdbj.org/pub/pdb/validation_reports/cg/8cgw | HTTPS FTP |
-Related structure data
Related structure data | 8cgpC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 100398.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LNPEP, OTASE / Production host: Homo sapiens (human) / References: UniProt: Q9UIQ6, cystinyl aminopeptidase |
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-Sugars , 5 types, 23 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #5: Polysaccharide | #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 82 molecules
#6: Chemical | #7: Chemical | ChemComp-UJX / | #9: Chemical | ChemComp-PEG / | #10: Chemical | #11: Chemical | ChemComp-GLY / #12: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.15 % |
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Crystal grow | Temperature: 278.15 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1M MMT (Malic acid, MES, Tris) 25% w/v PEG 1500 20% EG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 3.03→51.36 Å / Num. obs: 42729 / % possible obs: 92.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 78.87 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04135 / Rpim(I) all: 0.04135 / Net I/σ(I): 13.17 |
Reflection shell | Resolution: 3.03→3.138 Å / Rmerge(I) obs: 0.3287 / Num. unique obs: 3519 / CC1/2: 0.703 / Rpim(I) all: 0.3287 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.03→51.36 Å / SU ML: 0.4509 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.8097 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.03→51.36 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 35.6175495224 Å / Origin y: 0.782597267956 Å / Origin z: 13.3996187796 Å
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Refinement TLS group | Selection details: all |