+Open data
-Basic information
Entry | Database: PDB / ID: 4yfi | ||||||
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Title | TNNI3K complexed with inhibitor 1 | ||||||
Components | Serine/threonine-protein kinase TNNI3K | ||||||
Keywords | Transferase/Transferase Inhibitor / kinase / Transferase-Transferase Inhibitor complex | ||||||
Function / homology | Function and homology information bundle of His cell to Purkinje myocyte communication / regulation of cardiac muscle contraction / regulation of cardiac conduction / regulation of heart rate / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding ...bundle of His cell to Purkinje myocyte communication / regulation of cardiac muscle contraction / regulation of cardiac conduction / regulation of heart rate / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Shewchuk, L.M. / Wang, L. / Lawhorn, B.G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Identification of Purines and 7-Deazapurines as Potent and Selective Type I Inhibitors of Troponin I-Interacting Kinase (TNNI3K). Authors: Lawhorn, B.G. / Philp, J. / Zhao, Y. / Louer, C. / Hammond, M. / Cheung, M. / Fries, H. / Graves, A.P. / Shewchuk, L. / Wang, L. / Cottom, J.E. / Qi, H. / Zhao, H. / Totoritis, R. / Zhang, G. ...Authors: Lawhorn, B.G. / Philp, J. / Zhao, Y. / Louer, C. / Hammond, M. / Cheung, M. / Fries, H. / Graves, A.P. / Shewchuk, L. / Wang, L. / Cottom, J.E. / Qi, H. / Zhao, H. / Totoritis, R. / Zhang, G. / Schwartz, B. / Li, H. / Sweitzer, S. / Holt, D.A. / Gatto, G.J. / Kallander, L.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yfi.cif.gz | 424.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yfi.ent.gz | 349 KB | Display | PDB format |
PDBx/mmJSON format | 4yfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yfi_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4yfi_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4yfi_validation.xml.gz | 39.9 KB | Display | |
Data in CIF | 4yfi_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/4yfi ftp://data.pdbj.org/pub/pdb/validation_reports/yf/4yfi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 37267.977 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 503-831 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNNI3K, CARK / Plasmid: pFASTBAC / Production host: unidentified baculovirus References: UniProt: Q59H18, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-4CW / #3: Water | ChemComp-HOH / | |
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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: 2.86 Å3/Da / Density % sol: 57.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.3 M NaK tartrate, 0.1M HEPES pH7 |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 30, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 50917 / % possible obs: 97.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Χ2: 2.6 / Net I/av σ(I): 27.241 / Net I/σ(I): 18.7 / Num. measured all: 185934 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 2.7→37.82 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 22.659 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.602 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.99 Å2 / Biso mean: 48.295 Å2 / Biso min: 7.45 Å2
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Refinement step | Cycle: final / Resolution: 2.7→37.82 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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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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