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Yorodumi- PDB-4bdk: Fragment-based screening identifies a new area for inhibitor bind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bdk | ||||||
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Title | Fragment-based screening identifies a new area for inhibitor binding to checkpoint kinase 2 (CHK2) | ||||||
Components | CHECKPOINT KINASE 2 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information mitotic DNA damage checkpoint signaling / 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 / mitotic spindle assembly / replicative senescence / 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 ...mitotic DNA damage checkpoint signaling / 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 / mitotic spindle assembly / replicative senescence / 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 / Regulation of TP53 Activity through Methylation / cellular response to gamma radiation / PML body / G2/M transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / Regulation of TP53 Degradation / 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 / cell division / protein phosphorylation / 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 / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Silva-Santisteban, M.C. / Westwood, I.M. / Boxall, K. / Brown, N. / Peacock, S. / McAndrew, C. / Barrie, E. / Richards, M. / Mirza, A. / Oliver, A.W. ...Silva-Santisteban, M.C. / Westwood, I.M. / Boxall, K. / Brown, N. / Peacock, S. / McAndrew, C. / Barrie, E. / Richards, M. / Mirza, A. / Oliver, A.W. / Burke, R. / Hoelder, S. / Jones, K. / Aherne, G.W. / Blagg, J. / Collins, I. / Garrett, M.D. / van Montfort, R.L.M. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Fragment-Based Screening Maps Inhibitor Interactions in the ATP-Binding Site of Checkpoint Kinase 2. Authors: Silva-Santisteban, M.C. / Westwood, I.M. / Boxall, K. / Brown, N. / Peacock, S. / Mcandrew, C. / Barrie, E. / Richards, M. / Mirza, A. / Oliver, A.W. / Burke, R. / Hoelder, S. / Jones, K. / ...Authors: Silva-Santisteban, M.C. / Westwood, I.M. / Boxall, K. / Brown, N. / Peacock, S. / Mcandrew, C. / Barrie, E. / Richards, M. / Mirza, A. / Oliver, A.W. / Burke, R. / Hoelder, S. / Jones, K. / Aherne, G.W. / Blagg, J. / Collins, I. / Garrett, M.D. / Van Montfort, R.L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bdk.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bdk.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bdk_validation.pdf.gz | 464.4 KB | Display | wwPDB validaton report |
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Full document | 4bdk_full_validation.pdf.gz | 465.7 KB | Display | |
Data in XML | 4bdk_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 4bdk_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/4bdk ftp://data.pdbj.org/pub/pdb/validation_reports/bd/4bdk | HTTPS FTP |
-Related structure data
Related structure data | 4bdaC 4bdbC 4bdcC 4bddC 4bdeC 4bdfC 4bdgC 4bdhC 4bdiC 4bdjC 2wtjS S: Starting model for refinement C: citing same article (ref.) |
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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): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS References: UniProt: O96017, non-specific serine/threonine protein kinase | ||
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#2: Chemical | ChemComp-RQQ / | ||
#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: 3.54 Å3/Da / Density % sol: 64.99 % / Description: NONE |
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Crystal grow | Details: 0.1 M HEPES 7.5, 0.2 M MG(NO3)2, 10% (V/V) ETHYLENE GLYCOL, 1 MM TCEP AND 8-14% (W/V) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54189 |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jul 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54189 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→45.5 Å / Num. obs: 6975 / % possible obs: 99.5 % / Observed criterion σ(I): 1.5 / Redundancy: 8.3 % / Biso Wilson estimate: 50.76 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WTJ Resolution: 3.3→45.5 Å / Cor.coef. Fo:Fc: 0.9054 / Cor.coef. Fo:Fc free: 0.8416 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.432
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Displacement parameters | Biso mean: 49.58 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→45.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.69 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 25.2438 Å / Origin y: -29.5361 Å / Origin z: 10.2214 Å
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Refinement TLS group | Selection details: CHAIN A |