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- PDB-3kab: Structure-guided design of alpha-amino acid-derived Pin1 inhibitors -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kab | ||||||
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Title | Structure-guided design of alpha-amino acid-derived Pin1 inhibitors | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | ||||||
![]() | ISOMERASE / SBDD / PPIASE / ROTAMASE / SMALL MOLECULE / Proline directed kinase / cell cycle / Oncogenic transformation / Nucleus / Phosphoprotein | ||||||
Function / homology | ![]() cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / negative regulation of SMAD protein signal transduction ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / protein peptidyl-prolyl isomerization / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / : / ciliary basal body / positive regulation of GTPase activity / regulation of cytokinesis / negative regulation of protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / synapse organization / regulation of protein phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein stability / tau protein binding / negative regulation of protein catabolic process / neuron differentiation / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / positive regulation of protein phosphorylation / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Baker, L.M. / Dokurno, P. / Robinson, D.A. / Surgenor, A.E. / Murray, J.B. / Potter, A.J. / Moore, J.D. | ||||||
![]() | ![]() Title: Structure-guided design of alpha-amino acid-derived Pin1 inhibitors Authors: Potter, A.J. / Ray, S. / Gueritz, L. / Nunns, C.L. / Bryant, C.J. / Scrace, S.F. / Matassova, N. / Baker, L.M. / Dokurno, P. / Robinson, D.A. / Surgenor, A.E. / Davis, B. / Murray, J.B. / ...Authors: Potter, A.J. / Ray, S. / Gueritz, L. / Nunns, C.L. / Bryant, C.J. / Scrace, S.F. / Matassova, N. / Baker, L.M. / Dokurno, P. / Robinson, D.A. / Surgenor, A.E. / Davis, B. / Murray, J.B. / Richardson, C.M. / Moore, J.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 | ![]() | 47.7 KB | Display | ![]() |
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PDB format | ![]() | 31.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3kacC ![]() 3kadC ![]() 3kafC ![]() 3kagC ![]() 3kahC ![]() 3kaiC ![]() 3kceC ![]() 1pinS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18524.525 Da / Num. of mol.: 1 / Mutation: R14A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-12P / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-4BL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.2M Ammonium sulphate, 0.1M HEPES buffer, 1% PEG 400, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 5, 2005 / Details: mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→27.8 Å / Num. all: 11393 / Num. obs: 11393 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1025 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PIN Resolution: 2.19→27.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.785 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.197 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.34 Å2 / Biso mean: 44.793 Å2 / Biso min: 18.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→27.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.193→2.25 Å / Total num. of bins used: 20
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