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Yorodumi- PDB-7z28: High-resolution crystal structure of ERAP1 with bound bestatin an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z28 | ||||||
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Title | High-resolution crystal structure of ERAP1 with bound bestatin analogue inhibitor | ||||||
Components | Endoplasmic reticulum aminopeptidase 1 | ||||||
Keywords | HYDROLASE / Erap1 / Aminopeptidase / Zinc / metallopeptidase / bestatin / bestatin analogue / inhibitor | ||||||
Function / homology | Function and homology information interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / regulation of innate immune response / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis ...interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / regulation of innate immune response / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide binding / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / positive regulation of angiogenesis / angiogenesis / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Giastas, P. / Papakyriakou, A. / Stratikos, E. / Vourloumis, D. | ||||||
Funding support | Greece, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Discovery of Selective Nanomolar Inhibitors for Insulin-Regulated Aminopeptidase Based on alpha-Hydroxy-beta-amino Acid Derivatives of Bestatin. Authors: Vourloumis, D. / Mavridis, I. / Athanasoulis, A. / Temponeras, I. / Koumantou, D. / Giastas, P. / Mpakali, A. / Magrioti, V. / Leib, J. / van Endert, P. / Stratikos, E. / Papakyriakou, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z28.cif.gz | 385 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z28.ent.gz | 307.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z28_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7z28_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7z28_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 7z28_validation.cif.gz | 64.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/7z28 ftp://data.pdbj.org/pub/pdb/validation_reports/z2/7z28 | HTTPS FTP |
-Related structure data
Related structure data | 7zyfC 6q4rS S: Starting model for refinement 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 98405.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Bestatin analogue inhibitor / Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154 Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: Q9NZ08, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 904 molecules
#4: Chemical | ChemComp-ZN / | ||||||
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#5: Chemical | ChemComp-I88 / | ||||||
#6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-MLT / | #8: Chemical | ChemComp-PGE / | #9: Water | ChemComp-HOH / | |
-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: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG 7.0 25 % w/v PEG 1500 |
-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: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→88.05 Å / Num. obs: 132999 / % possible obs: 99.61 % / Observed criterion σ(F): 1.33 / Redundancy: 12 % / CC1/2: 0.75 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.55→1.57 Å / Rmerge(I) obs: 0.654 / Num. unique obs: 4161 / CC1/2: 0.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q4R Resolution: 1.55→88.05 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.83 / Stereochemistry target values: ML
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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 max: 91.65 Å2 / Biso mean: 24.1324 Å2 / Biso min: 11.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→88.05 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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