+Open data
-Basic information
Entry | Database: PDB / ID: 6cqe | ||||||
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Title | Crystal structure of HPK1 kinase domain S171A mutant | ||||||
Components | Mitogen-activated protein kinase kinase kinase kinase 1 | ||||||
Keywords | TRANSFERASE / Protein kinase | ||||||
Function / homology | Function and homology information MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / cell population proliferation / positive regulation of MAPK cascade / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation ...MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / cell population proliferation / positive regulation of MAPK cascade / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.886 Å | ||||||
Authors | Wu, P. / Lehoux, I. / Mortara, K. / Franke, Y. / Wang, W. | ||||||
Citation | Journal: Structure / Year: 2019 Title: Hematopoietic Progenitor Kinase-1 Structure in a Domain-Swapped Dimer. Authors: Wu, P. / Sneeringer, C.J. / Pitts, K.E. / Day, E.S. / Chan, B.K. / Wei, B. / Lehoux, I. / Mortara, K. / Li, H. / Wu, J. / Franke, Y. / Moffat, J.G. / Grogan, J.L. / Heffron, T.P. / Wang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cqe.cif.gz | 231.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cqe.ent.gz | 185.9 KB | Display | PDB format |
PDBx/mmJSON format | 6cqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/6cqe ftp://data.pdbj.org/pub/pdb/validation_reports/cq/6cqe | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32976.281 Da / Num. of mol.: 2 / Mutation: S171A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K1, HPK1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q92918, non-specific serine/threonine protein kinase #2: 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: 2.5 Å3/Da / Density % sol: 50.81 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl, pH 8.5, 0.25 M sodium tartrate, 12% PEG8000 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 14, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 54162 / % possible obs: 100 % / Redundancy: 6 % / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.9→1.96 Å |
-Processing
Software |
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Refinement | Resolution: 1.886→49.495 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.037 Å2 / ksol: 0.345 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.886→49.495 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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