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Yorodumi- PDB-4rc2: Crystal structure of Ser/Thr kinase Pim1 in complex with Mitoxant... -
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-Basic information
Entry | Database: PDB / ID: 4rc2 | ||||||
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Title | Crystal structure of Ser/Thr kinase Pim1 in complex with Mitoxantrone derivatives | ||||||
Components | Serine/threonine-protein kinase pim-1 | ||||||
Keywords | SIGNALING PROTEIN / kinase / phosphorylation | ||||||
Function / homology | Function and homology information positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / protein serine/threonine kinase activator activity / regulation of transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.096 Å | ||||||
Authors | Zhang, W. / Wan, X. / Huang, N. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Ser/Thr kinase Pim1 in complex with Mitoxantrone derivatives Authors: Zhang, W. / Wan, X. / Huang, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rc2.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rc2.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rc2_validation.pdf.gz | 738.6 KB | Display | wwPDB validaton report |
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Full document | 4rc2_full_validation.pdf.gz | 743.7 KB | Display | |
Data in XML | 4rc2_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4rc2_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/4rc2 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/4rc2 | HTTPS FTP |
-Related structure data
Related structure data | 4rblC 4rc3C 4rc4C 1ywvS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 33292.719 Da / Num. of mol.: 1 / Fragment: UNP Residues 29-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P11309, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-3O8 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 0.4 M potassium sodium tartrate tetrahydrate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97622 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2013 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 2.096→50 Å / Num. all: 25977 / Num. obs: 25977 / % possible obs: 99.7 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.082 |
Reflection shell | Resolution: 2.096→2.14 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.554 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YWV Resolution: 2.096→37.53 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.265 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 41.426 Å2
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Refinement step | Cycle: LAST / Resolution: 2.096→37.53 Å
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Refine LS restraints |
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