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Yorodumi- PDB-5n5l: Crystal structure of human Pim-1 kinase in complex with a consens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n5l | ||||||
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Title | Crystal structure of human Pim-1 kinase in complex with a consensuspeptide and [2-oxo-2-(1H-pyrrol-2-yl)ethyl] 5-bromo-1H-indole-3-carboxylate | ||||||
Components |
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Keywords | TRANSFERASE / Serine Threonine Kinase / proto-oncogene / Fragment / PIM-1 / Consensus peptide | ||||||
Function / homology | Function and homology information 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 / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response ...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 / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / positive regulation of TORC1 signaling / 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 / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Siefker, C. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: to be published Title: A crystallographic fragment study with human Pim-1 kinase Authors: Siefker, C. / Heine, A. / Taylor, C. / Kolb, P. / Hardes, K. / Steinmetzer, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n5l.cif.gz | 132.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n5l.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 5n5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n5l_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 5n5l_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 5n5l_validation.xml.gz | 14 KB | Display | |
Data in CIF | 5n5l_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/5n5l ftp://data.pdbj.org/pub/pdb/validation_reports/n5/5n5l | HTTPS FTP |
-Related structure data
Related structure data | 5mzlC 5n4nC 5n4oC 5n4rC 5n4uC 5n4vC 5n4xC 5n4yC 5n4zC 5n50C 5n51C 5n52C 5n5mC 5ndtC 3we8S 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: 35712.578 Da / Num. of mol.: 1 / Mutation: R250G Source method: isolated from a genetically manipulated source Details: Isofrom 2 of PIM-1 kinase Phosphorylation of Ser261 Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pLIC-SGC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS 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.) Homo sapiens (human) |
#3: Chemical | ChemComp-8NZ / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % / Description: hexagonal rod |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: HEPES Li2SO4 Glycerol DTT BIS-TRIS-propane PEG3350 Ethylene-glycol DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 16, 2016 / Details: Silicon |
Radiation | Monochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 30857 / % possible obs: 99.9 % / Redundancy: 6.84 % / CC1/2: 0.99 / Rrim(I) all: 0.076 / Net I/σ(I): 16.63 |
Reflection shell | Resolution: 1.97→2.09 Å / Redundancy: 6.58 % / Mean I/σ(I) obs: 3.17 / Num. unique obs: 4956 / CC1/2: 0.89 / Rrim(I) all: 0.57 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WE8 Resolution: 1.97→48.835 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→48.835 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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