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Yorodumi- PDB-1p2a: The structure of cyclin dependent kinase 2 (CKD2) with a trisubst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p2a | ||||||
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Title | The structure of cyclin dependent kinase 2 (CKD2) with a trisubstituted naphthostyril inhibitor | ||||||
Components | Cell division protein kinase 2 | ||||||
Keywords | TRANSFERASE / cyclin dependent kinase / naphthostyril oxindole | ||||||
Function / homology | Function and homology information Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich ...Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Liu, J.-J. / Dermatakis, A. / Lukacs, C.M. / Konzelmann, F. / Chen, Y. / Kammlott, U. / Depinto, W. / Yang, H. / Yin, X. / Chen, Y. ...Liu, J.-J. / Dermatakis, A. / Lukacs, C.M. / Konzelmann, F. / Chen, Y. / Kammlott, U. / Depinto, W. / Yang, H. / Yin, X. / Chen, Y. / Schutt, A. / Simcox, M.E. / Luk, K.-C. | ||||||
Citation | Journal: BIOORG.MED.CHEM. / Year: 2003 Title: 3,5,6-Trisubstituted Naphthostyrils as CDK2 Inhibitors Authors: Liu, J.-J. / Dermatakis, A. / Lukacs, C.M. / Konzelmann, F. / Chen, Y. / Kammlott, U. / Depinto, W. / Yang, H. / Yin, X. / Chen, Y. / Schutt, A. / Simcox, M.E. / Luk, K.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p2a.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p2a.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 1p2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p2a_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 1p2a_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 1p2a_validation.xml.gz | 8 KB | Display | |
Data in CIF | 1p2a_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/1p2a ftp://data.pdbj.org/pub/pdb/validation_reports/p2/1p2a | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | The biological assembly is the monomer |
-Components
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2 / Production host: unidentified baculovirus References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical | ChemComp-5BN / |
#3: 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: 2.01 Å3/Da / Density % sol: 38.8 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 3350, ammonium phosphate, bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 K / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 9514 / Num. obs: 9514 / % possible obs: 93.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.071 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique all: 802 / Rsym value: 0.111 / % possible all: 81.7 |
Reflection | *PLUS Lowest resolution: 40 Å / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.6 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.208 / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.208 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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