+Open data
-Basic information
Entry | Database: PDB / ID: 2m9i | ||||||
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Title | NMR solution structure of Pin1 WW domain variant 6-1 | ||||||
Components | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | ||||||
Keywords | ISOMERASE / N-glycosylation / Enhanced Aromatic Sequon / WW domain / CH-pi interaction | ||||||
Function / homology | Function and homology information 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 / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / 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 / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / protein peptidyl-prolyl isomerization / positive regulation of protein dephosphorylation / ciliary basal body / 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 / neuron differentiation / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of GTPase activity / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / protein stabilization / response to hypoxia / nuclear speck / positive regulation of protein phosphorylation / cell cycle / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Enck, S. / Chen, W. / Price, J.L. / Powers, E.T. / Wong, C. / Dyson, H.J. / Kelly, J.W. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Structural and energetic basis of carbohydrate-aromatic packing interactions in proteins. Authors: Chen, W. / Enck, S. / Price, J.L. / Powers, D.L. / Powers, E.T. / Wong, C.H. / Dyson, H.J. / Kelly, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m9i.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m9i.ent.gz | 172 KB | Display | PDB format |
PDBx/mmJSON format | 2m9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/2m9i ftp://data.pdbj.org/pub/pdb/validation_reports/m9/2m9i | HTTPS FTP |
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-Related structure data
Related structure data | 2m9eC 2m9fC 2m9jC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4022.507 Da / Num. of mol.: 1 / Fragment: MODIFIED WW DOMAIN (UNP RESIDUES 6-39) / Mutation: S11F, S14N, R16T, W29F / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13526 |
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Sequence details | THIS IS A PIN1 WW DOMAIN VARIANT |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 500 uM Pin WW Domain Peptide, 50 mM sodium phosphate, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||
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Sample |
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Sample conditions | Ionic strength: 0.08 / pH: 6.5 / Pressure: ambient / Temperature: 285 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | |||||||||
NMR constraints | NOE constraints total: 289 / NOE intraresidue total count: 50 / NOE long range total count: 121 / NOE medium range total count: 46 / NOE sequential total count: 72 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 19 |