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Yorodumi- PDB-7pfs: Crystal structure of ERAP2 aminopeptidase in complex with phosphi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pfs | ||||||
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Title | Crystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide ((1R)-1-Amino-3-phenylpropyl){2-([1,1:3,1-terphenyl]-5-ylmethyl)-3-[((2S)-1-amino-1-oxo-3-phenylpropan-2-yl)-amino]-3-oxopropyl}phosphinic acid | ||||||
Components | Endoplasmic reticulum aminopeptidase 2 | ||||||
Keywords | HYDROLASE / ERAP2 / transition state analogues / antigen presentation / phosphinic pseudotripeptides / aminopeptidase | ||||||
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: 2.7 Å | ||||||
Authors | Giastas, P. / Stratikos, E. / Mpakali, A. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2022 Title: Inhibitor-Dependent Usage of the S1' Specificity Pocket of ER Aminopeptidase 2. Authors: Mpakali, A. / Georgiadis, D. / Stratikos, E. / Giastas, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pfs.cif.gz | 905.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pfs.ent.gz | 627.6 KB | Display | PDB format |
PDBx/mmJSON format | 7pfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pfs_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 7pfs_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 7pfs_validation.xml.gz | 71.4 KB | Display | |
Data in CIF | 7pfs_validation.cif.gz | 96.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/7pfs ftp://data.pdbj.org/pub/pdb/validation_reports/pf/7pfs | HTTPS FTP |
-Related structure data
Related structure data | 7p7pC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 111010.820 Da / Num. of mol.: 2 / Mutation: K392N 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, 17 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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 #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 #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 88 molecules
#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-IMD / | #9: Chemical | #10: 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: 2.92 Å3/Da / Density % sol: 57.86 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02M of each monosaccharide (0.2M D-glucose, 0.2M D-mannose, 0.2M D-galactose,0.2M L-fucose, 0.2M D-xylose, 0.2M N-acetyl-D-glucosamine), 0.1M MES/imidazole pH 6.5 |
-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: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→65.03 Å / Num. obs: 61923 / % possible obs: 88.6 % / Redundancy: 2 % / Biso Wilson estimate: 65.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0441 / Rpim(I) all: 0.0441 / Net I/σ(I): 10.76 |
Reflection shell | Resolution: 2.7→2.797 Å / Mean I/σ(I) obs: 1.72 / Num. unique obs: 3318 / CC1/2: 0.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AB0 Resolution: 2.7→65.03 Å / SU ML: 0.4013 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.1083 / Stereochemistry target values: 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→65.03 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: 19.1468887638 Å / Origin y: 3.06791744566 Å / Origin z: 30.3394671441 Å
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Refinement TLS group | Selection details: all |