+Open data
-Basic information
Entry | Database: PDB / ID: 5o45 | ||||||||||||
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Title | Structure of human PD-L1 in complex with inhibitor | ||||||||||||
Components |
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Keywords | CELL CYCLE / PD-1 / Programmed Death 1 / PD-L1 / Programmed Death Ligand 1 / immune checkpoint / cancer | ||||||||||||
Function / homology | Function and homology information positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / PD-1 signaling / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å | ||||||||||||
Authors | Magiera, K. / Grudnik, P. / Dubin, G. / Holak, T.A. | ||||||||||||
Funding support | Poland, 3items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Bioactive Macrocyclic Inhibitors of the PD-1/PD-L1 Immune Checkpoint. Authors: Magiera-Mularz, K. / Skalniak, L. / Zak, K.M. / Musielak, B. / Rudzinska-Szostak, E. / Kocik, J. / Grudnik, P. / Sala, D. / Zarganes-Tzitzikas, T. / Shaabani, S. / Domling, A. / Dubin, G. / Holak, T.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o45.cif.gz | 125.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o45.ent.gz | 98.7 KB | Display | PDB format |
PDBx/mmJSON format | 5o45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/5o45 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/5o45 | HTTPS FTP |
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-Related structure data
Related structure data | 5o4yC 5c3tS 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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Unit cell |
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-Components
#1: Protein | Mass: 14792.861 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7 |
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#2: Protein/peptide | Mass: 1813.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M imidazole malate (pH 8.5) 27% PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 0.99→44.735 Å / Num. obs: 73554 / % possible obs: 94.29 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 0.99→1.025 Å / Rmerge(I) obs: 0.887 / CC1/2: 0.723 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5c3t Resolution: 0.99→44.735 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.11 Å2 / Biso mean: 16.6353 Å2 / Biso min: 5.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 0.99→44.735 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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