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Yorodumi- PDB-5lmk: Structure of phopsho-CDK2-cyclin A in complex with an ATP-competi... -
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-Basic information
Entry | Database: PDB / ID: 5lmk | ||||||
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Title | Structure of phopsho-CDK2-cyclin A in complex with an ATP-competitive inhibitor | ||||||
Components |
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Keywords | TRANSFERASE / CDK2 / cyclin A / cell cycle / inhibitor / complex | ||||||
Function / homology | Function and homology information G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Regulation of APC/C activators between G1/S and early anaphase ...G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Regulation of APC/C activators between G1/S and early anaphase / cellular response to leptin stimulus / male pronucleus / Telomere Extension By Telomerase / G0 and Early G1 / female pronucleus / response to glucagon / cellular response to cocaine / cellular response to nitric oxide / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cochlea development / cellular response to platelet-derived growth factor stimulus / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / regulation of DNA replication / animal organ regeneration / post-translational protein modification / cellular response to estradiol stimulus / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / Regulation of TP53 Degradation / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / Ub-specific processing proteases / protein domain specific binding / cell division / centrosome / DNA-templated transcription / positive regulation of DNA-templated transcription / protein kinase binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Echalier, A. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2016 Title: Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines. Authors: Hylsova, M. / Carbain, B. / Fanfrlik, J. / Musilova, L. / Haldar, S. / Kopruluoglu, C. / Ajani, H. / Brahmkshatriya, P.S. / Jorda, R. / Krystof, V. / Hobza, P. / Echalier, A. / Paruch, K. / Lepsik, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lmk.cif.gz | 232.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lmk.ent.gz | 184.7 KB | Display | PDB format |
PDBx/mmJSON format | 5lmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lmk_validation.pdf.gz | 972.3 KB | Display | wwPDB validaton report |
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Full document | 5lmk_full_validation.pdf.gz | 982.3 KB | Display | |
Data in XML | 5lmk_validation.xml.gz | 40.5 KB | Display | |
Data in CIF | 5lmk_validation.cif.gz | 56.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/5lmk ftp://data.pdbj.org/pub/pdb/validation_reports/lm/5lmk | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
-Cyclin-dependent kinase ... , 2 types, 2 molecules AC
#1: Protein | Mass: 34143.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase |
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#3: Protein | Mass: 33873.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase |
-Protein , 1 types, 2 molecules BD
#2: Protein | Mass: 29624.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P20248 |
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-Non-polymers , 4 types, 235 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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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: 2.94 Å3/Da / Density % sol: 58.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: ammonium sulphate; potassium chloride; sodium Hepes pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→99.95 Å / Num. obs: 253641 / % possible obs: 98.7 % / Redundancy: 4.3 % / Net I/σ(I): 13.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CDK2?cyclin A structure Resolution: 2.4→99.94 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.494 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.247
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.22 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→99.94 Å
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