[English] 日本語
Yorodumi- PDB-4b9d: Crystal Structure of Human NIMA-related Kinase 1 (NEK1) with inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b9d | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human NIMA-related Kinase 1 (NEK1) with inhibitor. | ||||||
Components | SERINE/THREONINE-PROTEIN KINASE NEK1 | ||||||
Keywords | TRANSFERASE / INHIBITOR | ||||||
Function / homology | Function and homology information cell cycle / pericentriolar material / centriolar satellite / cilium assembly / 14-3-3 protein binding / kinase activity / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation ...cell cycle / pericentriolar material / centriolar satellite / cilium assembly / 14-3-3 protein binding / kinase activity / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / 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: 1.9 Å | ||||||
Authors | Elkins, J.M. / Hanchuk, T.D.M. / Lovato, D.V. / Basei, F.L. / Meirelles, G.V. / Kobarg, J. / Szklarz, M. / Vollmar, M. / Mahajan, P. / Rellos, P. ...Elkins, J.M. / Hanchuk, T.D.M. / Lovato, D.V. / Basei, F.L. / Meirelles, G.V. / Kobarg, J. / Szklarz, M. / Vollmar, M. / Mahajan, P. / Rellos, P. / Zhang, Y. / Krojer, T. / Pike, A.C.W. / Canning, P. / von Delft, F. / Raynor, J. / Bountra, C. / Arrowsmith, C. / Edwards, A. / Knapp, S. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: NEK1 kinase domain structure and its dynamic protein interactome after exposure to Cisplatin. Authors: Melo-Hanchuk, T.D. / Slepicka, P.F. / Meirelles, G.V. / Basei, F.L. / Lovato, D.V. / Granato, D.C. / Pauletti, B.A. / Domingues, R.R. / Leme, A.F.P. / Pelegrini, A.L. / Lenz, G. / Knapp, S. ...Authors: Melo-Hanchuk, T.D. / Slepicka, P.F. / Meirelles, G.V. / Basei, F.L. / Lovato, D.V. / Granato, D.C. / Pauletti, B.A. / Domingues, R.R. / Leme, A.F.P. / Pelegrini, A.L. / Lenz, G. / Knapp, S. / Elkins, J.M. / Kobarg, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4b9d.cif.gz | 252.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4b9d.ent.gz | 202.8 KB | Display | PDB format |
PDBx/mmJSON format | 4b9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b9d_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4b9d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4b9d_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 4b9d_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/4b9d ftp://data.pdbj.org/pub/pdb/validation_reports/b9/4b9d | HTTPS FTP |
-Related structure data
Related structure data | 4apcSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: -20 - 283 / Label seq-ID: 4 - 305
NCS oper: (Code: given Matrix: (0.06184, 0.99803, 0.01031), Vector: |
-Components
#1: Protein | Mass: 39912.066 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 1-328 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96PY6, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 0.2M NA/KPO4, 20% PEG 3350, 10% ETHYLENE GLYCOL, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.18 Å / Num. obs: 52249 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.4 / % possible all: 93.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4APC Resolution: 1.9→45.22 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.281 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.598 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→45.22 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|