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Yorodumi- PDB-8poi: Molecular Docking of SPF30 Tudor domain with synthetic inhibitor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8poi | |||||||||
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Title | Molecular Docking of SPF30 Tudor domain with synthetic inhibitor 4-(pyridin-2-yl)thiazol-2-amine | |||||||||
Components | Survival of motor neuron-related-splicing factor 30 | |||||||||
Keywords | RNA BINDING PROTEIN / tudor domain / complex / inhibitor | |||||||||
Function / homology | Function and homology information RNA splicing, via transesterification reactions / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / Cajal body / mRNA Splicing - Major Pathway / mRNA processing / nuclear speck / apoptotic process / RNA binding / nucleoplasm ...RNA splicing, via transesterification reactions / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / Cajal body / mRNA Splicing - Major Pathway / mRNA processing / nuclear speck / apoptotic process / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Borggraefe, J. / Gaussmann, S. / Sattler, M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Pharmacological perturbation of the phase-separating protein SMNDC1. Authors: Enders, L. / Siklos, M. / Borggrafe, J. / Gaussmann, S. / Koren, A. / Malik, M. / Tomek, T. / Schuster, M. / Reinis, J. / Hahn, E. / Rukavina, A. / Reicher, A. / Casteels, T. / Bock, C. / ...Authors: Enders, L. / Siklos, M. / Borggrafe, J. / Gaussmann, S. / Koren, A. / Malik, M. / Tomek, T. / Schuster, M. / Reinis, J. / Hahn, E. / Rukavina, A. / Reicher, A. / Casteels, T. / Bock, C. / Winter, G.E. / Hannich, J.T. / Sattler, M. / Kubicek, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8poi.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8poi.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 8poi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/8poi ftp://data.pdbj.org/pub/pdb/validation_reports/po/8poi | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6935.511 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMNDC1, SMNR, SPF30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O75940 |
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#2: Chemical | ChemComp-ZTI / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1 mM [U-13C; U-15N] SPF30(65-128), 20 mM NA- cmp13, 20 mM NA- sodium phosphate, 50 mM NA- NaCl, 5 mM NA- DTT, 100% D2O Details: 1mM 15N,13C-SPF30(65-128) + 20mM cmp13 in 20mM NaPi pH 6.5, 50mM NaCl, 5mM DTT, lyophiized and resuspended in D2O Label: SPF30_cmp13 / Solvent system: 100% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 70 mM / Label: conditons_D20 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz / Details: H/N/C triple-resonance cryogenic probe |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | ||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 400 / Conformers submitted total number: 4 |