+Open data
-Basic information
Entry | Database: PDB / ID: 7akm | ||||||
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Title | Crystal structure of CHK1 kinase domain in complex with ATPyS | ||||||
Components | Serine/threonine-protein kinase Chk1 | ||||||
Keywords | CELL CYCLE | ||||||
Function / homology | Function and homology information negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / negative regulation of mitotic nuclear division / mitotic G2/M transition checkpoint / regulation of mitotic centrosome separation / nucleus organization / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / negative regulation of mitotic nuclear division / mitotic G2/M transition checkpoint / regulation of mitotic centrosome separation / nucleus organization / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic / cellular response to caffeine / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of cell cycle / Activation of ATR in response to replication stress / signal transduction in response to DNA damage / DNA damage checkpoint signaling / replication fork / regulation of signal transduction by p53 class mediator / condensed nuclear chromosome / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / G2/M DNA damage checkpoint / Signaling by SCF-KIT / cellular response to mechanical stimulus / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / chromatin remodeling / protein domain specific binding / protein phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / DNA repair / protein serine/threonine kinase activity / centrosome / apoptotic process / DNA damage response / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Day, M. / Oliver, A.W. / Pearl, L.H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Structure / Year: 2021 Title: Structural basis for recruitment of the CHK1 DNA damage kinase by the CLASPIN scaffold protein. Authors: Day, M. / Parry-Morris, S. / Houghton-Gisby, J. / Oliver, A.W. / Pearl, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7akm.cif.gz | 284.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7akm.ent.gz | 184.9 KB | Display | PDB format |
PDBx/mmJSON format | 7akm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/7akm ftp://data.pdbj.org/pub/pdb/validation_reports/ak/7akm | HTTPS FTP |
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-Related structure data
Related structure data | 7akoC 1ia8S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34213.219 Da / Num. of mol.: 2 / Mutation: D10R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O14757, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 448 molecules
#2: Chemical | ChemComp-AGS / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CIT / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.97 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 200 mM Sodium citrate tribasic dihydrate, 100 mM Bis-Tris propane pH 8.5 and 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96864 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→44.63 Å / Num. obs: 49422 / % possible obs: 98.35 % / Redundancy: 4 % / Biso Wilson estimate: 28.6 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1555 / Rpim(I) all: 0.08786 / Rrim(I) all: 0.1795 / Net I/σ(I): 5.57 |
Reflection shell | Resolution: 1.93→1.999 Å / Rmerge(I) obs: 1.313 / Mean I/σ(I) obs: 0.79 / Num. unique obs: 4447 / CC1/2: 0.336 / Rpim(I) all: 0.7813 / Rsym value: 1.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IA8 Resolution: 1.93→44.63 Å / SU ML: 0.2459 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2472
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→44.63 Å
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Refine LS restraints |
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LS refinement shell |
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