+Open data
-Basic information
Entry | Database: PDB / ID: 2wtd | ||||||
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Title | Crystal structure of Chk2 in complex with an inhibitor | ||||||
Components | SERINE/THREONINE-PROTEIN KINASE CHK2 | ||||||
Keywords | TRANSFERASE / KINASE / CELL CYCLE / LI-FRAUMENI SYNDROME | ||||||
Function / homology | Function and homology information mitotic DNA damage checkpoint signaling / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / replicative senescence / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage ...mitotic DNA damage checkpoint signaling / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / replicative senescence / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / protein catabolic process / G2/M DNA damage checkpoint / PML body / cellular response to gamma radiation / Regulation of TP53 Activity through Methylation / intrinsic apoptotic signaling pathway in response to DNA damage / G2/M transition of mitotic cell cycle / Regulation of TP53 Degradation / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / DNA damage response / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Hilton, S. / Naud, S. / Caldwell, J.J. / Boxall, K. / Burns, S. / Anderson, V.E. / Antoni, L. / Allen, C.E. / Pearl, L.H. / Oliver, A.W. ...Hilton, S. / Naud, S. / Caldwell, J.J. / Boxall, K. / Burns, S. / Anderson, V.E. / Antoni, L. / Allen, C.E. / Pearl, L.H. / Oliver, A.W. / Aherne, G.W. / Garrett, M.D. / Collins, I. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2010 Title: Identification and Characterisation of 2-Aminopyridine Inhibitors of Checkpoint Kinase 2 Authors: Hilton, S. / Naud, S. / Caldwell, J.J. / Boxall, K. / Burns, S. / Anderson, V.E. / Antoni, L. / Allen, C.E. / Pearl, L.H. / Oliver, A.W. / Aherne, G.W. / Garrett, M.D. / Collins, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wtd.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wtd.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wtd_validation.pdf.gz | 702.1 KB | Display | wwPDB validaton report |
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Full document | 2wtd_full_validation.pdf.gz | 707.9 KB | Display | |
Data in XML | 2wtd_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 2wtd_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/2wtd ftp://data.pdbj.org/pub/pdb/validation_reports/wt/2wtd | HTTPS FTP |
-Related structure data
Related structure data | 2wtcC 2wtiC 2wtjC 2cn5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37111.844 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 210-531 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTHREE-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS References: UniProt: O96017, non-specific serine/threonine protein kinase | ||
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#2: Chemical | ChemComp-ZZK / | ||
#3: Chemical | ChemComp-NO3 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.91 % / Description: NONE |
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Crystal grow | Details: 0.1 M HEPES PH 7.5, 0.2 M MAGNESIUM NITRATE, 8-16% (W/V) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 10, 2009 Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→60.04 Å / Num. obs: 11882 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.35 % / Biso Wilson estimate: 64.18 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.45 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.58 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CN5 Resolution: 2.75→39.98 Å / SU ML: 1.1 / σ(F): 1.5 / Phase error: 25.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.96 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.75→39.98 Å
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Refine LS restraints |
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LS refinement shell |
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