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Open data
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Basic information
Entry | Database: PDB / ID: 8s9h | ||||||
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Title | Crystal structure of monkey TLR7 ectodomain with compound 14 | ||||||
![]() | Toll-like receptor 7![]() | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() toll-like receptor 7 signaling pathway / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Critton, D.A. | ||||||
Funding support | 1items
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![]() | ![]() Title: Identification and Optimization of Small Molecule Pyrazolopyrimidine TLR7 Agonists for Applications in Immuno-oncology. Authors: He, L. / Zhang, M.Y. / Cox, M. / Zhang, Q. / Donnell, A.F. / Zhang, Y. / Tarby, C. / Gill, P. / Subbaiah, M.A.M. / Ramar, T. / Reddy, M. / Puttapaka, V. / Li, Y.X. / Sivaprakasam, P. / ...Authors: He, L. / Zhang, M.Y. / Cox, M. / Zhang, Q. / Donnell, A.F. / Zhang, Y. / Tarby, C. / Gill, P. / Subbaiah, M.A.M. / Ramar, T. / Reddy, M. / Puttapaka, V. / Li, Y.X. / Sivaprakasam, P. / Critton, D. / Mulligan, D. / Xie, C. / Ramakrishnan, R. / Nagar, J. / Dudhgaonkar, S. / Murtaza, A. / Oderinde, M.S. / Schieven, G.L. / Mathur, A. / Gavai, A.V. / Vite, G. / Gangwar, S. / Poudel, Y.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 916.7 KB | Display | ![]() |
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PDB format | ![]() | 779.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 94014.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Sugars , 3 types, 18 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 3 types, 715 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | Mass: 538.685 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H42N8O3 / Feature type: SUBJECT OF INVESTIGATION #6: Chemical | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2 ammonium citrate pH 5.0, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.437→101.703 Å / Num. obs: 59766 / % possible obs: 94.7 % / Redundancy: 5.74 % / CC1/2: 0.991 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.437→2.681 Å / Num. unique obs: 2988 / CC1/2: 0.543 |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
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Displacement parameters | Biso mean: 53.24 Å2
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.437→35.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.44→2.6 Å / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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