+Open data
-Basic information
Entry | Database: PDB / ID: 8s9h | ||||||
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Title | Crystal structure of monkey TLR7 ectodomain with compound 14 | ||||||
Components | Toll-like receptor 7 | ||||||
Keywords | IMMUNE SYSTEM / Toll-like receptor 7 / pattern recognition receptor / agonist | ||||||
Function / homology | Function and homology information toll-like receptor 7 signaling pathway / pattern recognition receptor activity / toll-like receptor signaling pathway / canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / defense response to virus / inflammatory response / innate immune response / plasma membrane Similarity search - Function | ||||||
Biological species | Macaca mulatta (Rhesus monkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.437 Å | ||||||
Authors | Critton, D.A. | ||||||
Funding support | 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s9h.cif.gz | 916.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s9h.ent.gz | 779.6 KB | Display | PDB format |
PDBx/mmJSON format | 8s9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/8s9h ftp://data.pdbj.org/pub/pdb/validation_reports/s9/8s9h | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Macaca mulatta (Rhesus monkey) / Gene: TLR7 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: G8E2R2 |
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-Sugars , 3 types, 18 molecules
#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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å |
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: 0.979 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.437→35.32 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.173 / SU Rfree Blow DPI: 0.338 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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