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- PDB-8e5m: Structure of ARG1 complex with pyrrolidine-based non-boronic acid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8e5m | ||||||
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Title | Structure of ARG1 complex with pyrrolidine-based non-boronic acid inhibitor 6 | ||||||
![]() | Arginase-1 | ||||||
![]() | HYDROLASE/INHIBITOR / Arginase / hydrolase / urea cycle / metabolism / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation ...positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation / arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Palte, R.L. / Gathiaka, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Discovery of non-boronic acid Arginase 1 inhibitors through virtual screening and biophysical methods. Authors: Gathiaka, S. / Palte, R.L. / So, S.S. / Chai, X. / Richard Miller, J. / Kuvelkar, R. / Wen, X. / Cifelli, S. / Kreamer, A. / Liaw, A. / McLaren, D.G. / Fischer, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 393.1 KB | Display | ![]() |
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PDB format | ![]() | 318.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 77.4 KB | Display | |
Data in CIF | ![]() | 108.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8e5nC ![]() 6v7cS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34779.879 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-UKR / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% MMT (pH 7.0), 0.1 ammonium formate, 16-22% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→71.88 Å / Num. obs: 158294 / % possible obs: 91.4 % / Redundancy: 3.4 % / CC1/2: 0.997 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.84→1.875 Å / Num. unique obs: 28817 / CC1/2: 0.739 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6V7C Resolution: 1.84→71.52 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.139
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Displacement parameters | Biso max: 124.11 Å2 / Biso mean: 29 Å2 / Biso min: 9.52 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.84→71.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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