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Open data
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Basic information
Entry | Database: PDB / ID: 7k4j | |||||||||
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Title | Human Arginase 1 in complex with compound 51. | |||||||||
![]() | Arginase-1 | |||||||||
![]() | HYDROLASE/HYDROLASE inhibitor / Arginase / hydrolase / arginine / urea cycle / inhibitor / HYDROLASE-HYDROLASE inhibitor complex | |||||||||
Function / homology | ![]() positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / Urea cycle / arginase / arginase activity / : / urea cycle / response to nematode / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan ...positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / Urea cycle / arginase / arginase activity / : / urea cycle / response to nematode / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Palte, R.L. | |||||||||
![]() | ![]() Title: Comprehensive Strategies to Bicyclic Prolines: Applications in the Synthesis of Potent Arginase Inhibitors. Authors: Li, D. / Zhang, H. / Lyons, T.W. / Lu, M. / Achab, A. / Pu, Q. / Childers, M. / Mitcheltree, M.J. / Wang, J. / Martinot, T.A. / McMinn, S.E. / Sloman, D.L. / Palani, A. / Beard, A. / Nogle, ...Authors: Li, D. / Zhang, H. / Lyons, T.W. / Lu, M. / Achab, A. / Pu, Q. / Childers, M. / Mitcheltree, M.J. / Wang, J. / Martinot, T.A. / McMinn, S.E. / Sloman, D.L. / Palani, A. / Beard, A. / Nogle, L. / Gathiaka, S. / Sauri, J. / Kim, H.Y. / Adpressa, D. / Spacciapoli, P. / Miller, J.R. / Palte, R.L. / Lesburg, C.A. / Cumming, J. / 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 | ![]() | 384.5 KB | Display | ![]() |
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PDB format | ![]() | 311.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 73.2 KB | Display | |
Data in CIF | ![]() | 103.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7k4gC ![]() 7k4hC ![]() 7k4iC ![]() 7k4kC ![]() 6v7dS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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-VV1 / #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: 50.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% MMT (pH 7.0) 0.1 M ammonium formate, 16-22% PEG 80 |
-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: Aug 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→67.38 Å / Num. obs: 131620 / % possible obs: 88.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 21.95 Å2 / CC1/2: 0.992 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.94→2.05 Å / Num. unique obs: 19063 / CC1/2: 0.881 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6V7D Resolution: 1.94→67.38 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.813 / SU R Cruickshank DPI: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.198 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.176
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Displacement parameters | Biso max: 110.39 Å2 / Biso mean: 24.73 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→67.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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