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Yorodumi- PDB-5j6s: Crystal structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j6s | |||||||||
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Title | Crystal structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in complex with a hydroxamic derivative ligand | |||||||||
Components | Endoplasmic reticulum aminopeptidase 2 | |||||||||
Keywords | HYDROLASE / Endoplasmic reticulum / aminopeptidase / Zn binding metallopeptidase | |||||||||
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 / adaptive immune response / endopeptidase activity / 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: 2.8 Å | |||||||||
Authors | Saridakis, E. / Giastas, P. / Mpakali, A. / Deprez-Poulain, R. / Stratikos, E. | |||||||||
Funding support | Greece, 1items
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Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: Crystal Structures of ERAP2 Complexed with Inhibitors Reveal Pharmacophore Requirements for Optimizing Inhibitor Potency. Authors: Mpakali, A. / Giastas, P. / Deprez-Poulain, R. / Papakyriakou, A. / Koumantou, D. / Gealageas, R. / Tsoukalidou, S. / Vourloumis, D. / Mavridis, I.M. / Stratikos, E. / Saridakis, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j6s.cif.gz | 385.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j6s.ent.gz | 311.3 KB | Display | PDB format |
PDBx/mmJSON format | 5j6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j6s_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 5j6s_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 5j6s_validation.xml.gz | 68 KB | Display | |
Data in CIF | 5j6s_validation.cif.gz | 91.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/5j6s ftp://data.pdbj.org/pub/pdb/validation_reports/j6/5j6s | HTTPS FTP |
-Related structure data
Related structure data | 5k1vC 5ab0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 111563.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP2, LRAP / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q6P179, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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-Sugars , 4 types, 16 molecules
#2: Polysaccharide | #3: Polysaccharide | #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 53 molecules
#5: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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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: 2.82 Å3/Da / Density % sol: 56.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.3 Details: 7 %(w/v) PEG 8000, 20 %(v/v) ethylene glycol, 59 mM MES, 41 mM imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.99987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→73.51 Å / Num. obs: 60772 / % possible obs: 99.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.7 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AB0 Resolution: 2.8→73.507 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→73.507 Å
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Refine LS restraints |
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LS refinement shell |
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