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Yorodumi- PDB-1pxi: HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR 4-(2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pxi | ||||||
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Title | HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR 4-(2,5-Dichloro-thiophen-3-yl)-pyrimidin-2-ylamine | ||||||
Components | Cell division protein kinase 2 | ||||||
Keywords | TRANSFERASE / PROTEIN KINASE / CELL CYCLE / PHOSPHORYLATION / CELL DIVISION / MITOSIS / INHIBITION / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / 3D-STRUCTURE. | ||||||
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: 1.95 Å | ||||||
Authors | Wu, S.Y. / McNae, I. / Kontopidis, G. / McClue, S.J. / McInnes, C. / Stewart, K.J. / Wang, S. / Zheleva, D.I. / Marriage, H. / Lane, D.P. ...Wu, S.Y. / McNae, I. / Kontopidis, G. / McClue, S.J. / McInnes, C. / Stewart, K.J. / Wang, S. / Zheleva, D.I. / Marriage, H. / Lane, D.P. / Taylor, P. / Fischer, P.M. / Walkinshaw, M.D. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Discovery of a novel family of CDK inhibitors with the program LIDAEUS: structural basis for ligand-induced disordering of the activation loop Authors: Wu, S.Y. / McNae, I. / Kontopidis, G. / McClue, S.J. / McInnes, C. / Stewart, K.J. / Wang, S. / Zheleva, D.I. / Marriage, H. / Lane, D.P. / Taylor, P. / Fischer, P.M. / Walkinshaw, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pxi.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pxi.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pxi_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 1pxi_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 1pxi_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 1pxi_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/1pxi ftp://data.pdbj.org/pub/pdb/validation_reports/px/1pxi | HTTPS FTP |
-Related structure data
Related structure data | 1pw2C 1pxjC 1pxkC 1pxlC 1hclS 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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Unit cell |
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-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: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical | ChemComp-CK1 / |
#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: 2.03 Å3/Da / Density % sol: 39.49 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG 6000, NA-HEPES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 8.2 / PH range high: 7.8 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 20770 / Num. obs: 20770 / % possible obs: 98.8 % / Redundancy: 12.05 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.95→1.98 Å / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 6.61 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 253672 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HCL Resolution: 1.95→19.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1552241.76 / Data cutoff high rms absF: 1552241.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 37 - 40 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.8169 Å2 / ksol: 0.345562 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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