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Yorodumi- PDB-7zun: Crystal structure of PIM1 in complex with a Pyrrolo-Pyrazinone co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zun | |||||||||
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Title | Crystal structure of PIM1 in complex with a Pyrrolo-Pyrazinone compound | |||||||||
Components | Isoform 2 of Serine/threonine-protein kinase pim-1 | |||||||||
Keywords | TRANSFERASE / PIM1 / ATP BINDING / KINASE INHIBITOR | |||||||||
Function / homology | non-specific serine/threonine protein kinase / Chem-JYO / Isoform 2 of Serine/threonine-protein kinase pim-1 Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Casale, E. | |||||||||
Funding support | 1items
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Citation | Journal: Chirality / Year: 2022 Title: Stereoselective synthesis of 3,4-dihydropyrrolo[1,2-a]pyrazin-1(2H)-one derivatives as PIM kinase inhibitors inspired from marine alkaloids. Authors: Casuscelli, F. / Ardini, E. / Avanzi, N. / Badari, A. / Casale, E. / Disingrini, T. / Donati, D. / Ermoli, A. / Felder, E.R. / Galvani, A. / Isacchi, A. / Menichincheri, M. / Montemartini, M. ...Authors: Casuscelli, F. / Ardini, E. / Avanzi, N. / Badari, A. / Casale, E. / Disingrini, T. / Donati, D. / Ermoli, A. / Felder, E.R. / Galvani, A. / Isacchi, A. / Menichincheri, M. / Montemartini, M. / Orrenius, C. / Piutti, C. / Salom, B. / Papeo, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zun.cif.gz | 122.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zun.ent.gz | 92.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zun_validation.pdf.gz | 844.7 KB | Display | wwPDB validaton report |
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Full document | 7zun_full_validation.pdf.gz | 845.9 KB | Display | |
Data in XML | 7zun_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 7zun_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/7zun ftp://data.pdbj.org/pub/pdb/validation_reports/zu/7zun | HTTPS FTP |
-Related structure data
Related structure data | 1yhsS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35835.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: residue SEP 261 is a PHOSPHOSERINE THE FIRST TWO RESIDUES AT THE N-TERMINAL GLY AND PRO ARE EXPRESSION TAG Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli) References: UniProt: P11309-2, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-JYO / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.6 / Details: 20% PEG 3350K, 0.3 M NACL, 0.1 M TRIS-HCL PH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→36.7 Å / Num. obs: 14258 / % possible obs: 99.3 % / Redundancy: 4.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 6771 / CC1/2: 0.807 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YHS Resolution: 2.5→36.655 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.666 / SU ML: 0.189 / Cross valid method: FREE R-VALUE / ESU R: 0.317 / ESU R Free: 0.245 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.926 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→36.655 Å
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Refine LS restraints |
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LS refinement shell |
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