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Yorodumi- PDB-7fqj: Crystal Structure of human Legumain in complex with (2S)-N-[(1S)-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fqj | |||||||||
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Title | Crystal Structure of human Legumain in complex with (2S)-N-[(1S)-3-amino-1-cyano-3-oxopropyl]-1-[1-[4-[(2,4-difluorophenyl)methoxy]phenyl]cyclopropanecarbonyl]pyrrolidine-2-carboxamide | |||||||||
Components | Legumain | |||||||||
Keywords | HYDROLASE/INHIBITOR / CYSTEINE PROTEASE / ALLOSTERIC INHIBITOR / ASPARAGINYL ENDOPEPTIDASE / ALZHEIMER'S DISEASE / HYDROLASE / HYDROLASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / endolysosome lumen / response to acidic pH ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / endolysosome lumen / response to acidic pH / activation of cysteine-type endopeptidase activity / dendritic spine organization / positive regulation of monocyte chemotaxis / Trafficking and processing of endosomal TLR / positive regulation of endothelial cell chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / protein maturation / endopeptidase activator activity / cellular response to calcium ion / MHC class II antigen presentation / positive regulation of mitotic cell cycle / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of long-term synaptic potentiation / tau protein binding / memory / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / apical part of cell / peptidase activity / negative regulation of neuron apoptotic process / lysosome / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Ehler, A. / Benz, J. / Bartels, B. / Rudolph, M.G. | |||||||||
Funding support | Switzerland, 1items
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Citation | Journal: To be published Title: Crystal Structure of a human Legumain complex Authors: Bartels, B. / Kuhn, B. / Benz, J. / Rudolph, M.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fqj.cif.gz | 200.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fqj.ent.gz | 154 KB | Display | PDB format |
PDBx/mmJSON format | 7fqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fqj_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7fqj_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7fqj_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 7fqj_validation.cif.gz | 54.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/7fqj ftp://data.pdbj.org/pub/pdb/validation_reports/fq/7fqj | HTTPS FTP |
-Group deposition
ID | G_1002245 (5 entries) |
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Title | To be published |
Type | undefined |
Description | A set of AEP_Legumain crystal structures |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 50877.672 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGMN, PRSC1 / Plasmid: pExpreS2.1_hLGMN(18-433)_C-VD-8xHis / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): ExpreS2 / References: UniProt: Q99538, legumain |
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-Sugars , 2 types, 3 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 |
-Non-polymers , 8 types, 676 molecules
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PG4 / | #7: Chemical | ChemComp-EPE / | #8: Chemical | ChemComp-FLC / | #9: Chemical | ChemComp-MG / | #10: Chemical | ChemComp-SO4 / | #11: 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: 2.01 Å3/Da / Density % sol: 38.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 25.7mg/mL protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 20% v/v PEG smear high, ...Details: 25.7mg/mL protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 20% v/v PEG smear high, 0.15M Li2SO4, 0.05M MgCL2, 0.1M HEPES/NaOH pH 7.8, total volume 200nL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99982 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99982 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→112.62 Å / Num. obs: 128574 / % possible obs: 99 % / Redundancy: 3.02 % / Biso Wilson estimate: 35.81 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.32 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3 % / Rmerge(I) obs: 2.079 / Mean I/σ(I) obs: 0.49 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INHOUSE MODEL Resolution: 1.7→112.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.341 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: WITH A MG2+-CITRATE COMPLEX BOUND
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→112.62 Å
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