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Yorodumi- PDB-6y8k: Crystal structure of CD137 in complex with the cyclic peptide BCY10916 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y8k | ||||||
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Title | Crystal structure of CD137 in complex with the cyclic peptide BCY10916 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / TNFRSF9 / CD137 / 4-1BB / bicyclic peptide / Bicycle / BCY10916 | ||||||
Function / homology | Function and homology information TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / signaling receptor activity / regulation of cell population proliferation / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.011 Å | ||||||
Authors | Upadhyaya, P. / Kublin, J. / Dods, R. / Kristensson, J. / Lahdenranta, J. / Kleyman, M. / Repash, E. / Ma, J. / Mudd, G. / Van Rietschoten, K. ...Upadhyaya, P. / Kublin, J. / Dods, R. / Kristensson, J. / Lahdenranta, J. / Kleyman, M. / Repash, E. / Ma, J. / Mudd, G. / Van Rietschoten, K. / Haines, E. / Harrison, H. / Beswick, P. / Chen, L. / McDonnell, K. / Battula, S. / Hurov, K. / Keen, N. | ||||||
Citation | Journal: J Immunother Cancer / Year: 2021 Title: Anticancer immunity induced by a synthetic tumor-targeted CD137 agonist. Authors: Upadhyaya, P. / Lahdenranta, J. / Hurov, K. / Battula, S. / Dods, R. / Haines, E. / Kleyman, M. / Kristensson, J. / Kublin, J. / Lani, R. / Ma, J. / Mudd, G. / Repash, E. / Van Rietschoten, ...Authors: Upadhyaya, P. / Lahdenranta, J. / Hurov, K. / Battula, S. / Dods, R. / Haines, E. / Kleyman, M. / Kristensson, J. / Kublin, J. / Lani, R. / Ma, J. / Mudd, G. / Repash, E. / Van Rietschoten, K. / Stephen, T. / You, F. / Harrison, H. / Chen, L. / McDonnell, K. / Brandish, P. / Keen, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y8k.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y8k.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6y8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/6y8k ftp://data.pdbj.org/pub/pdb/validation_reports/y8/6y8k | HTTPS FTP |
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-Related structure data
Related structure data | 6mi2S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AAAPPP
#1: Protein | Mass: 17765.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF9, CD137, ILA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q07011 |
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#2: Protein/peptide | Mass: 1753.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BCY10916 / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 6 types, 37 molecules
#3: Chemical | ChemComp-ACT / | ||||||
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#4: Chemical | ChemComp-EDO / | ||||||
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-29N / | #8: Water | ChemComp-HOH / | |
-Details
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: 3.92 Å3/Da / Density % sol: 68.63 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 4.6 Details: 1.5 M lithium sulfate monohydrate, 0.1M sodium acetate trihydrate, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→40.857 Å / Num. obs: 21496 / % possible obs: 100 % / Redundancy: 39.1 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.043 / Net I/σ(I): 45.7 |
Reflection shell | Resolution: 2.01→2.05 Å / Rmerge(I) obs: 2.216 / Num. unique obs: 1053 / CC1/2: 0.756 / Rrim(I) all: 2.244 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MI2 Resolution: 2.011→40.857 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: FREE R-VALUE / ESU R: 0.156 / ESU R Free: 0.152 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.013 Å2
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Refinement step | Cycle: LAST / Resolution: 2.011→40.857 Å
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Refine LS restraints |
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LS refinement shell |
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