+Open data
-Basic information
Entry | Database: PDB / ID: 7siu | ||||||
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Title | Crystal structure of HPK1 (MAP4K1) complex with inhibitor A-745 | ||||||
Components | Mitogen-activated protein kinase kinase kinase kinase 1 | ||||||
Keywords | SIGNALING PROTEIN / 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 / MOLECULAR REPLACEMENT / Resolution: 1.786 Å | ||||||
Authors | Longenecker, K.L. / Korepanova, A. / Qiu, W. | ||||||
Funding support | 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2022 Title: The HPK1 Inhibitor A-745 Verifies the Potential of Modulating T Cell Kinase Signaling for Immunotherapy. Authors: Malchow, S. / Korepanova, A. / Panchal, S.C. / McClure, R.A. / Longenecker, K.L. / Qiu, W. / Zhao, H. / Cheng, M. / Guo, J. / Klinge, K.L. / Trusk, P. / Pratt, S.D. / Li, T. / Kurnick, M.D. ...Authors: Malchow, S. / Korepanova, A. / Panchal, S.C. / McClure, R.A. / Longenecker, K.L. / Qiu, W. / Zhao, H. / Cheng, M. / Guo, J. / Klinge, K.L. / Trusk, P. / Pratt, S.D. / Li, T. / Kurnick, M.D. / Duan, L. / Shoemaker, A.R. / Gopalakrishnan, S.M. / Warder, S.E. / Shotwell, J.B. / Lai, A. / Sun, C. / Osuma, A.T. / Pappano, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7siu.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7siu.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 7siu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/7siu ftp://data.pdbj.org/pub/pdb/validation_reports/si/7siu | HTTPS FTP |
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-Related structure data
Related structure data | 3ggfS S: Starting model for refinement |
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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: 34693.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K1, HPK1 / Cell line (production host): HEK (293-6E) / Production host: Homo sapiens (human) References: UniProt: Q92918, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.81 Å3/Da / Density % sol: 56.15 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG1000, 100 mM Li2SO4, 100 mM Sodium Citrate, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.786→80.9 Å / Num. obs: 75564 / % possible obs: 98.9 % / Redundancy: 11 % / Biso Wilson estimate: 26.27 Å2 / Rpim(I) all: 0.029 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.787→1.817 Å / Num. unique obs: 3293 / Rpim(I) all: 0.405 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ggf Resolution: 1.786→80.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.097
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Displacement parameters | Biso max: 88.65 Å2 / Biso mean: 29.2 Å2 / Biso min: 12.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.786→80.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.8 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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