[English] 日本語
![](img/lk-miru.gif)
- PDB-4bda: Fragment-based screening identifies a new area for inhibitor bind... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4bda | ||||||
---|---|---|---|---|---|---|---|
Title | Fragment-based screening identifies a new area for inhibitor binding to checkpoint kinase 2 (CHK2) | ||||||
![]() | SERINE/THREONINE-PROTEIN KINASE CHK2 | ||||||
![]() | TRANSFERASE | ||||||
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 / 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 | ![]() | ||||||
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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 130.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 100.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 465.6 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bdbC ![]() 4bdcC ![]() 4bddC ![]() 4bdeC ![]() 4bdfC ![]() 4bdgC ![]() 4bdhC ![]() 4bdiC ![]() 4bdjC ![]() 4bdkC ![]() 2wtjS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#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, non-specific serine/threonine protein kinase |
---|
-Non-polymers , 5 types, 101 molecules ![](data/chem/img/NO3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/VFB.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/VFB.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NO3 / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-VFB / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 63.74 % / Description: NONE |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9728 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40.1 Å / Num. obs: 14123 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Biso Wilson estimate: 69.79 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WTJ Resolution: 2.6→22.68 Å / Cor.coef. Fo:Fc: 0.9479 / Cor.coef. Fo:Fc free: 0.9291 / SU R Cruickshank DPI: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.34 / SU Rfree Blow DPI: 0.25 / SU Rfree Cruickshank DPI: 0.25
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.44 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.323 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→22.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.81 Å / Total num. of bins used: 7
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -25.5177 Å / Origin y: 29.5974 Å / Origin z: 10.1996 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: CHAIN A |