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Yorodumi- PDB-2x4z: Crystal Structure of the Human p21-Activated Kinase 4 in Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x4z | |||||||||
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Title | Crystal Structure of the Human p21-Activated Kinase 4 in Complex with PF-03758309 | |||||||||
Components | SERINE/THREONINE-PROTEIN KINASE PAK 4 | |||||||||
Keywords | TRANSFERASE / NUCLEOTIDE-BINDING ATP-BINDING / PHOSPHOPROTEIN | |||||||||
Function / homology | Function and homology information dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / RHOG GTPase cycle / cellular response to organic cyclic compound / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / cytoskeleton organization / RAC1 GTPase cycle / regulation of cell growth / adherens junction / positive regulation of angiogenesis / cell migration / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cell cycle / phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / signal transduction / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Knighton, D.R. / Deng, Y. / Murray, B. / Guo, C. / Piraino, J. / Westwick, J. / Zhang, C. / Lamerdin, J. / Dagostino, E. / Loi, C.-M. ...Knighton, D.R. / Deng, Y. / Murray, B. / Guo, C. / Piraino, J. / Westwick, J. / Zhang, C. / Lamerdin, J. / Dagostino, E. / Loi, C.-M. / Zager, M. / Kraynov, E. / Christensen, J. / Martinez, R. / Kephart, S. / Marakovits, J. / Karlicek, S. / Bergqvist, S. / Smeal, T. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Small-Molecule P21-Activated Kinase Inhibitor Pf- 3758309 is a Potent Inhibitor of Oncogenic Signaling and Tumor Growth. Authors: Murray, B. / Guo, C. / Piraino, J. / Westwick, J. / Zhang, C. / Lamerdin, J. / Dagostino, E. / Knighton, D.R. / Loi, C.-M. / Zager, M. / Kraynov, E. / Popoff, I. / Christensen, J. / ...Authors: Murray, B. / Guo, C. / Piraino, J. / Westwick, J. / Zhang, C. / Lamerdin, J. / Dagostino, E. / Knighton, D.R. / Loi, C.-M. / Zager, M. / Kraynov, E. / Popoff, I. / Christensen, J. / Martinez, R. / Kephart, S. / Marakovits, J. / Karlicek, S. / Bergqvist, S. / Smeal, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x4z.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x4z.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 2x4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/2x4z ftp://data.pdbj.org/pub/pdb/validation_reports/x4/2x4z | HTTPS FTP |
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-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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-Components
#1: Protein | Mass: 33424.840 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 296-591 / Mutation: YES Source method: isolated from a genetically manipulated source Details: S474 IS PHOSPHORYLATED / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: O96013, non-specific serine/threonine protein kinase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-7KC / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, PRO 296 TO GLY ENGINEERED RESIDUE IN CHAIN A, GLN 296 TO SER ...ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.23 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRROR |
Radiation | Monochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 18889 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.95 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.15 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.51 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 38819.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.3793 Å2 / ksol: 0.378448 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→46.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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