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Yorodumi- PDB-7sh0: CRYSTAL STRUCTURE OF ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2 (ERAP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sh0 | ||||||
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Title | CRYSTAL STRUCTURE OF ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2 (ERAP2) COMPLEX WITH A HIGHLY SELECTIVE AND POTENT SMALL MOLECULE | ||||||
Components | Endoplasmic reticulum aminopeptidase 2 | ||||||
Keywords | IMMUNE SYSTEM / HYDROLASE/INHIBITOR / AMINOPEPTIDASE / ERAP2 STRUCTURE / ENZYME INHIBITOR / ANTIGEN PROCESSING / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / metallopeptidase activity ...Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / metallopeptidase activity / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / proteolysis / extracellular space / zinc ion binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Li, L. / Bouvier, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: Discovery of the First Selective Nanomolar Inhibitors of ERAP2 by Kinetic Target-Guided Synthesis. Authors: Camberlein, V. / Fleau, C. / Sierocki, P. / Li, L. / Gealageas, R. / Bosc, D. / Guillaume, V. / Warenghem, S. / Leroux, F. / Rosell, M. / Cheng, K. / Medve, L. / Prigent, M. / Decanter, M. / ...Authors: Camberlein, V. / Fleau, C. / Sierocki, P. / Li, L. / Gealageas, R. / Bosc, D. / Guillaume, V. / Warenghem, S. / Leroux, F. / Rosell, M. / Cheng, K. / Medve, L. / Prigent, M. / Decanter, M. / Piveteau, C. / Biela, A. / Eveque, M. / Dumont, J. / Mpakali, A. / Giastas, P. / Herledan, A. / Couturier, C. / Haupenthal, J. / Lesire, L. / Hirsch, A.K.H. / Deprez, B. / Stratikos, E. / Bouvier, M. / Deprez-Poulain, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sh0.cif.gz | 876.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sh0.ent.gz | 613.5 KB | Display | PDB format |
PDBx/mmJSON format | 7sh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sh0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7sh0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7sh0_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 7sh0_validation.cif.gz | 78.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/7sh0 ftp://data.pdbj.org/pub/pdb/validation_reports/sh/7sh0 | HTTPS FTP |
-Related structure data
Related structure data | 5kivS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper: (Code: givenMatrix: (-0.99938730817, -0.01402084863, -0.0320690516157), (-0.00537706383751, 0.966883714441, -0.25516067474), (0.0345846129417, -0.254831902542, -0.966366703687)Vector: 36. ...NCS oper: (Code: given Matrix: (-0.99938730817, -0.01402084863, -0.0320690516157), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 111563.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP2, LRAP / Plasmid: PFASTBAC-1 / Production host: Homo sapiens (human) References: UniProt: Q6P179, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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-Non-polymers , 6 types, 17 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EPE / | #5: Chemical | ChemComp-MES / #6: Chemical | ChemComp-NA / | #7: 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: 2.99 Å3/Da / Density % sol: 58.79 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 6.5 Details: 12% Ethylene glycol, 6% PEG8000;0.1m MES and imidazole PH range: 6.0-6.6 |
-Data collection
Diffraction | Mean temperature: 103 K / Ambient temp details: liguid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 2, 2021 |
Radiation | Monochromator: 0.97857 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. obs: 42605 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 103.33 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.132 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3.2→3.39 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1 / Num. unique obs: 6543 / CC1/2: 0.46 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5kiv Resolution: 3.2→20 Å / SU ML: 0.5645 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6195 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: 127.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 18.7670118375 Å / Origin y: 1.88376958218 Å / Origin z: 30.2391732231 Å
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Refinement TLS group | Selection details: all |