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Open data
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Basic information
Entry | Database: PDB / ID: 7uxq | ||||||
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Title | Structure of PDL1 in complex with FP28135, a Helicon Polypeptide | ||||||
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![]() | IMMUNE SYSTEM / Complex / stapled | ||||||
Function / homology | ![]() 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 | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, K. / Agarwal, S. / Tokareva, O. / Thomson, T. / Travaline, T. / Wahl, S. / Verdine, G. / McGee, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: De novo mapping of alpha-helix recognition sites on protein surfaces using unbiased libraries. Authors: Li, K. / Tokareva, O.S. / Thomson, T.M. / Wahl, S.C.T. / Travaline, T.L. / Ramirez, J.D. / Choudary, S.K. / Agarwal, S. / Walkup 4th, W.G. / Olsen, T.J. / Brennan, M.J. / Verdine, G.L. / McGee, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80 KB | Display | ![]() |
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PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482.4 KB | Display | ![]() |
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Full document | ![]() | 486.3 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uwiC ![]() 7uwoC ![]() 7ux5C ![]() 7uxiC ![]() 7uxjC ![]() 7uxkC ![]() 7uxmC ![]() 7uxnC ![]() 7uxoC ![]() 7uxpC ![]() 7uy2C ![]() 7uyjC ![]() 7uykC ![]() 4zqkS C: citing same article ( S: Starting model for refinement |
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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: 14809.955 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2015.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.15 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 1.1 M Sodium Malonate pH 7.0, 0.1 M HEPES pH 7.0, 0.5% v/v Jeffamine ED-2001 Reagent pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→48.38 Å / Num. obs: 13300 / % possible obs: 99.91 % / Redundancy: 83.4 % / Biso Wilson estimate: 76.94 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.382 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 2.89→2.99 Å / Num. unique obs: 1294 / CC1/2: 0.776 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZQK Resolution: 2.89→48.38 Å / SU ML: 0.3366 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.6943 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 74.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→48.38 Å
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Refine LS restraints |
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LS refinement shell |
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