+Open data
-Basic information
Entry | Database: PDB / ID: 5wvd | ||||||
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Title | Structure of Mnk1 in complex with DS12881479 | ||||||
Components | MAP kinase interacting serine/threonine kinase 1 | ||||||
Keywords | TRANSFERASE / kinase / kinase inhibitor / inactive conformation | ||||||
Function / homology | Function and homology information calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / Spry regulation of FGF signaling / regulation of translation / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / protein phosphorylation / protein serine kinase activity ...calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / Spry regulation of FGF signaling / regulation of translation / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Matsui, Y. / Hanzawa, H. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: A novel inhibitor stabilizes the inactive conformation of MAPK-interacting kinase 1. Authors: Matsui, Y. / Yasumatsu, I. / Yoshida, K.I. / Iimura, S. / Ikeno, Y. / Nawano, T. / Fukano, H. / Ubukata, O. / Hanzawa, H. / Tanzawa, F. / Isoyama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wvd.cif.gz | 199.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wvd.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 5wvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wvd_validation.pdf.gz | 858.9 KB | Display | wwPDB validaton report |
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Full document | 5wvd_full_validation.pdf.gz | 861.7 KB | Display | |
Data in XML | 5wvd_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 5wvd_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/5wvd ftp://data.pdbj.org/pub/pdb/validation_reports/wv/5wvd | HTTPS FTP |
-Related structure data
Related structure data | 2hw6S 5wvj 5wvl S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 34745.465 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 37-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MKNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: B5BUJ6, UniProt: Q9BUB5*PLUS #2: Chemical | ChemComp-SO4 / | #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: polyethylene glycol 3350, ammonium sulfate, citrate buffer (pH 6.2), MgCl2 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 15900 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HW6 Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.878 / SU B: 36.894 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R Free: 0.428
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.197 Å2
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Refinement step | Cycle: 1 / Resolution: 3→20 Å
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Refine LS restraints |
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