+Open data
-Basic information
Entry | Database: PDB / ID: 7k4h | |||||||||
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Title | Human Arginase 1 in complex with compound 04. | |||||||||
Components | Arginase-1 | |||||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / Arginase / hydrolase / arginine / urea cycle / inhibitor / HYDROLASE-HYDROLASE inhibitor complex | |||||||||
Function / homology | Function and homology information 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 / negative regulation of type II interferon-mediated signaling pathway / urea cycle / 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 / negative regulation of type II interferon-mediated signaling pathway / urea cycle / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Palte, R.L. | |||||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k4h.cif.gz | 402.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k4h.ent.gz | 324.4 KB | Display | PDB format |
PDBx/mmJSON format | 7k4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/7k4h ftp://data.pdbj.org/pub/pdb/validation_reports/k4/7k4h | HTTPS FTP |
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-Related structure data
Related structure data | 7k4gC 7k4iC 7k4jC 7k4kC 6v7eS 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
#1: Protein | Mass: 34779.879 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P05089, arginase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-VV4 / #4: Water | ChemComp-HOH / | 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: 2.44 Å3/Da / Density % sol: 49.57 % |
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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 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.645→71.523 Å / Num. obs: 218547 / % possible obs: 90.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 11.96 Å2 / CC1/2: 0.97 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.645→1.673 Å / Num. unique obs: 11371 / CC1/2: 0.731 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6V7E Resolution: 1.65→48.88 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.851 / SU R Cruickshank DPI: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.127 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.114
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Displacement parameters | Biso max: 131.45 Å2 / Biso mean: 13.48 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→48.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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