+Open data
-Basic information
Entry | Database: PDB / ID: 6v7c | ||||||
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Title | Human Arginase1 Complexed with Bicyclic Inhibitor Compound 3 | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / AGONIST / ARG (ARGINASE) / BICYCLIC / IMMUNOTHERAPY / METALLOENZYME / HYDROLASE / 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: 1.8 Å | ||||||
Authors | Palte, R.L. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2020 Title: Discovery and Optimization of Rationally Designed Bicyclic Inhibitors of Human Arginase to Enhance Cancer Immunotherapy. Authors: Mitcheltree, M.J. / Li, D. / Achab, A. / Beard, A. / Chakravarthy, K. / Cheng, M. / Cho, H. / Eangoor, P. / Fan, P. / Gathiaka, S. / Kim, H.Y. / Lesburg, C.A. / Lyons, T.W. / Martinot, T.A. ...Authors: Mitcheltree, M.J. / Li, D. / Achab, A. / Beard, A. / Chakravarthy, K. / Cheng, M. / Cho, H. / Eangoor, P. / Fan, P. / Gathiaka, S. / Kim, H.Y. / Lesburg, C.A. / Lyons, T.W. / Martinot, T.A. / Miller, J.R. / McMinn, S. / O'Neil, J. / Palani, A. / Palte, R.L. / Sauri, J. / Sloman, D.L. / Zhang, H. / Cumming, J.N. / Fischer, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v7c.cif.gz | 381.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v7c.ent.gz | 309 KB | Display | PDB format |
PDBx/mmJSON format | 6v7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v7c_validation.pdf.gz | 598 KB | Display | wwPDB validaton report |
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Full document | 6v7c_full_validation.pdf.gz | 599.5 KB | Display | |
Data in XML | 6v7c_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 6v7c_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/6v7c ftp://data.pdbj.org/pub/pdb/validation_reports/v7/6v7c | HTTPS FTP |
-Related structure data
Related structure data | 6v7dC 6v7eC 6v7fC 3gmzS 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 / Plasmid: pET24 / Cell (production host): BL21 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P05089, arginase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-QR1 / { #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: 49.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / 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: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→65.42 Å / Num. obs: 169488 / % possible obs: 94.5 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.805→1.811 Å / Rmerge(I) obs: 0.51 / Num. unique obs: 1767 / CC1/2: 0.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GMZ Resolution: 1.8→35.84 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.833 / SU R Cruickshank DPI: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.142 / SU Rfree Cruickshank DPI: 0.146
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Displacement parameters | Biso max: 100.29 Å2 / Biso mean: 16.92 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→35.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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