+Open data
-Basic information
Entry | Database: PDB / ID: 5dh3 | |||||||||
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Title | Crystal structure of MST2 in complex with XMU-MP-1 | |||||||||
Components | Serine/threonine-protein kinase 3Serine/threonine-specific protein kinase | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / MST2 / MST1 / Hippo Pathway / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome ...cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome / organ growth / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / canonical Wnt signaling pathway / positive regulation of fat cell differentiation / JNK cascade / protein serine/threonine kinase activator activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / epithelial cell proliferation / central nervous system development / protein tetramerization / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / protein import into nucleus / negative regulation of epithelial cell proliferation / positive regulation of protein binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / magnesium ion binding / signal transduction / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.468 Å | |||||||||
Authors | Kong, L.L. / Yun, C.H. | |||||||||
Funding support | China, 2items
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Citation | Journal: Sci Transl Med / Year: 2016 Title: Pharmacological targeting of kinases MST1 and MST2 augments tissue repair and regeneration Authors: Fan, F. / He, Z. / Kong, L.L. / Chen, Q. / Yuan, Q. / Zhang, S. / Ye, J. / Liu, H. / Sun, X. / Geng, J. / Yuan, L. / Hong, L. / Xiao, C. / Zhang, W. / Sun, X. / Li, Y. / Wang, P. / Huang, L. ...Authors: Fan, F. / He, Z. / Kong, L.L. / Chen, Q. / Yuan, Q. / Zhang, S. / Ye, J. / Liu, H. / Sun, X. / Geng, J. / Yuan, L. / Hong, L. / Xiao, C. / Zhang, W. / Sun, X. / Li, Y. / Wang, P. / Huang, L. / Wu, X. / Ji, Z. / Wu, Q. / Xia, N.S. / Gray, N.S. / Chen, L. / Yun, C.H. / Deng, X. / Zhou, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dh3.cif.gz | 132.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dh3.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 5dh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/5dh3 ftp://data.pdbj.org/pub/pdb/validation_reports/dh/5dh3 | HTTPS FTP |
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-Related structure data
Related structure data | 4lg4S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35739.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STK3, KRS1, MST2 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q13188, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis-Tris pH 6.5, 28% PEG3350, 0.2M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97861 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97861 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 26735 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.452 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LG4 Resolution: 2.468→47.217 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.08 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.468→47.217 Å
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Refine LS restraints |
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LS refinement shell |
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