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- PDB-5n4x: Crystal structure of human Pim-1 kinase in complex with a consens... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n4x | ||||||
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Title | Crystal structure of human Pim-1 kinase in complex with a consensuspeptide and fragment like molekule 4,5-dibromothiophene-2-carbohydrazide | ||||||
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![]() | TRANSFERASE / Serine Threonine Kinase / proto-oncogene / Fragment / PIM-1 / Consensus peptide | ||||||
Function / homology | ![]() positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / 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 / vitamin D receptor signaling pathway / cellular detoxification / 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 / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Siefker, C. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: A crystallographic fragment study with human Pim-1 kinase Authors: Siefker, C. / Heine, A. / Hardes, K. / Steinmetzer, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.5 KB | Display | ![]() |
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PDB format | ![]() | 98.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5mzlC ![]() 5n4nC ![]() 5n4oC ![]() 5n4rC ![]() 5n4uC ![]() 5n4vC ![]() 5n4yC ![]() 5n4zC ![]() 5n50C ![]() 5n51C ![]() 5n52C ![]() 5n5lC ![]() 5n5mC ![]() 5ndtC ![]() 3we8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35632.602 Da / Num. of mol.: 1 / Mutation: R250G Source method: isolated from a genetically manipulated source Details: Isofrom 2 of PIM-1 kinase / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11309, non-specific serine/threonine protein kinase |
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#2: Protein/peptide | Mass: 1592.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PIM-1 consensus peptide / Source: (synth.) ![]() |
#3: Chemical | ChemComp-8MT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 61 % / Description: hexagonal rod |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: HEPES MgCl2 Glycerol DTT BIS-TRIS-propane PEG3350 Ethylene-glycol DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2019 / Details: Silicon |
Radiation | Monochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 22535 / % possible obs: 99.9 % / Redundancy: 6.98 % / CC1/2: 0.99 / Rrim(I) all: 0.099 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.2→2.33 Å / Redundancy: 7.02 % / Mean I/σ(I) obs: 3.64 / Num. unique obs: 3603 / CC1/2: 0.89 / Rrim(I) all: 0.548 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WE8 Resolution: 2.2→49.004 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→49.004 Å
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Refine LS restraints |
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LS refinement shell |
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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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