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- PDB-4bde: Fragment-based screening identifies a new area for inhibitor bind... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bde | ||||||
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Title | Fragment-based screening identifies a new area for inhibitor binding to checkpoint kinase 2 (CHK2) | ||||||
![]() | SERINE/THREONINE-PROTEIN KINASE CHK2 | ||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129 KB | Display | ![]() |
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PDB format | ![]() | 99.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bdaC ![]() 4bdbC ![]() 4bdcC ![]() 4bddC ![]() 4bdfC ![]() 4bdgC ![]() 4bdhC ![]() 4bdiC ![]() 4bdjC ![]() 4bdkC ![]() 2wtjS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O96017, ![]() | ||||
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#2: Chemical | ChemComp-NO3 / ![]() | ||||
#3: Chemical | ChemComp-EDO / ![]() #4: Chemical | ChemComp-CWS / | #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.21 % / 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: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.55→60.19 Å / Num. obs: 14972 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 5.9 % / Biso Wilson estimate: 65.37 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2WTJ Resolution: 2.55→40.16 Å / Cor.coef. Fo:Fc: 0.9454 / Cor.coef. Fo:Fc free: 0.9413 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.306 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.215
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Displacement parameters | Biso mean: 57.87 Å2
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Refine analyze | Luzzati coordinate error obs: 0.318 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→40.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.73 Å / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: -25.2944 Å / Origin y: 29.5349 Å / Origin z: 10.2612 Å
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Refinement TLS group | Selection details: CHAIN A |