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- PDB-5kgg: Crystal structure of PIM1 with inhibitor: 2-(5-chloranyl-1~{H}-in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kgg | ||||||
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Title | Crystal structure of PIM1 with inhibitor: 2-(5-chloranyl-1~{H}-indol-3-yl)ethanamine | ||||||
![]() | Serine/threonine-protein kinase pim-1 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase / transferase / Serine/threonine-protein kinase pim-1 / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferguson, A.D. | ||||||
![]() | ![]() Title: Structure of PIM1 in complex with inhibitor Authors: Ferguson, A.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.8 KB | Display | ![]() |
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PDB format | ![]() | 102.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.1 KB | Display | ![]() |
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Full document | ![]() | 469.1 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 21.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kgdC ![]() 5kgeC ![]() 5kgiC ![]() 5kgkC ![]() 4dtkS C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31905.203 Da / Num. of mol.: 1 / Fragment: UNP residues 30-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11309, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 249 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/6SO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/6SO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-6SO / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 18% PEG 3350, 0.2 M Na2SO4, 6% ethylene glycol, 0.1 M Tris, pH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→24.97 Å / Num. obs: 31577 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 27.37 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 5.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DTK Resolution: 1.95→24.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.094
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Displacement parameters | Biso mean: 31.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.95→24.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Origin x: -30.4129 Å / Origin y: -27.3087 Å / Origin z: 0.303 Å
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Refinement TLS group | Selection details: { A|* } |