+Open data
-Basic information
Entry | Database: PDB / ID: 6tpa | ||||||
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Title | CDK8/CyclinC in complex with drug ETP-50775 | ||||||
Components |
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Keywords | CELL CYCLE / Cell division Kinase Inhibitor | ||||||
Function / homology | Function and homology information CKM complex / G0 to G1 transition / negative regulation of triglyceride metabolic process / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / RSV-host interactions / negative regulation of Notch signaling pathway / cyclin-dependent protein kinase holoenzyme complex ...CKM complex / G0 to G1 transition / negative regulation of triglyceride metabolic process / mediator complex / Generic Transcription Pathway / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / RSV-host interactions / negative regulation of Notch signaling pathway / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / ubiquitin ligase complex / RNA polymerase II CTD heptapeptide repeat kinase activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PPARA activates gene expression / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / ubiquitin protein ligase activity / protein kinase activity / protein ubiquitination / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Munoz, I.G. / Pastor, J. / Martinez, S. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2020 Title: Pyrido[2,3-b][1,5]benzoxazepin-5(6H)-one derivatives as CDK8 inhibitors. Authors: Martinez-Gonzalez, S. / Garcia, A.B. / Albarran, M.I. / Cebria, A. / Amezquita-Alves, A. / Garcia-Campos, F.J. / Martinez-Gago, J. / Martinez-Torrecuadrada, J. / Munoz, I. / Blanco-Aparicio, C. / Pastor, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tpa.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tpa.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 6tpa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tpa_validation.pdf.gz | 749.5 KB | Display | wwPDB validaton report |
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Full document | 6tpa_full_validation.pdf.gz | 766 KB | Display | |
Data in XML | 6tpa_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 6tpa_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/6tpa ftp://data.pdbj.org/pub/pdb/validation_reports/tp/6tpa | HTTPS FTP |
-Related structure data
Related structure data | 5ceiS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 46962.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK8 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P49336, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
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#2: Protein | Mass: 33479.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNC Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P24863 |
-Non-polymers , 4 types, 105 molecules
#3: Chemical | ChemComp-NZ8 / | ||||
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#4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-NZ5 / ( #6: 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: 3.06 Å3/Da / Density % sol: 59.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 200mM NaFormate, 3% Butanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 2.7998→94.564 Å / Num. obs: 24925 / % possible obs: 99.5 % / Redundancy: 5.5 % / CC1/2: 0.99 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.7998→2.91 Å / Num. unique obs: 1817 / CC1/2: 0.89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CEI Resolution: 2.8→94.564 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.85 Å2 / Biso mean: 50.7182 Å2 / Biso min: 23.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→94.564 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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