+Open data
-Basic information
Entry | Database: PDB / ID: 8tty | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of monkey TLR7 ectodomain with compound 5 | ||||||
Components | Toll-like receptor 7 | ||||||
Keywords | IMMUNE SYSTEM / Toll-like receptor 7 | ||||||
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: 2.101 Å | ||||||
Authors | Critton, D.A. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2024 Title: Discovery of Novel TLR7 Agonists as Systemic Agent for Combination With aPD1 for Use in Immuno-oncology. Authors: Poudel, Y.B. / He, L. / Cox, M. / Zhang, Q. / Johnson, W.L. / Cong, Q. / Cheng, H. / Chowdari, N.S. / Tarby, C. / Donnell, A.F. / Broekema, M. / O'Malley, D.P. / Zhang, Y. / A M Subbaiah, M. ...Authors: Poudel, Y.B. / He, L. / Cox, M. / Zhang, Q. / Johnson, W.L. / Cong, Q. / Cheng, H. / Chowdari, N.S. / Tarby, C. / Donnell, A.F. / Broekema, M. / O'Malley, D.P. / Zhang, Y. / A M Subbaiah, M. / Kumar, B.V. / Subramani, L. / Wang, B. / Li, Y.X. / Sivaprakasam, P. / Critton, D. / Mulligan, D. / Sandhu, B. / Xie, C. / Ramakrishnan, R. / Nagar, J. / Dudhgaonkar, S. / Oderinde, M.S. / Murtaza, A. / Schieven, G.L. / Mathur, A. / Gavai, A.V. / Vite, G. / Gangwar, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8tty.cif.gz | 929.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8tty.ent.gz | 790.8 KB | Display | PDB format |
PDBx/mmJSON format | 8tty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/8tty ftp://data.pdbj.org/pub/pdb/validation_reports/tt/8tty | HTTPS FTP |
---|
-Related structure data
Related structure data | 8ttzC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|
-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 | ||
---|---|---|---|
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 759 molecules
#5: Chemical | Mass: 409.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H31N7O / Feature type: SUBJECT OF INVESTIGATION #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.32 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M ammonium citrate, 0.1 M nickel (II) chloride, 20% (w/v) PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→102.21 Å / Num. obs: 97119 / % possible obs: 95.8 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.1→2.28 Å / Num. unique obs: 4856 / CC1/2: 0.571 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→102.21 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.263 / SU Rfree Blow DPI: 0.2 Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.67 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.101→102.21 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.101→2.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|