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- PDB-2jfl: CRYSTAL STRUCTURE OF HUMAN STE20-LIKE KINASE (DIPHOSPHORYLATED FO... -
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Basic information
Entry | Database: PDB / ID: 2jfl | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN STE20-LIKE KINASE (DIPHOSPHORYLATED FORM) BOUND TO 5- AMINO-3-((4-(AMINOSULFONYL)PHENYL)AMINO)-N-(2,6- DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE | ||||||
![]() | STE20-LIKE SERINE/THREONINE-PROTEIN KINASE | ||||||
![]() | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION / MUSCLE DEVELOPMENT / KINASE / APOPTOSIS / GERMINAL CENTRE KINASE / SERINE- THREONINE KINASE 2 / NUCLEOTIDE-BINDING / SERINE-THREONINE-PROTEIN KINASE | ||||||
Function / homology | ![]() regulation of focal adhesion assembly / RHOB GTPase cycle / cell leading edge / RHOC GTPase cycle / RHOA GTPase cycle / cytoplasmic microtubule organization / regulation of cell migration / regulation of apoptotic process / protein autophosphorylation / non-specific serine/threonine protein kinase ...regulation of focal adhesion assembly / RHOB GTPase cycle / cell leading edge / RHOC GTPase cycle / RHOA GTPase cycle / cytoplasmic microtubule organization / regulation of cell migration / regulation of apoptotic process / protein autophosphorylation / non-specific serine/threonine protein kinase / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pike, A.C.W. / Rellos, P. / Fedorov, O. / Keates, T. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Bunkoczi, G. / von Delft, F. / Arrowsmith, C.H. ...Pike, A.C.W. / Rellos, P. / Fedorov, O. / Keates, T. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Bunkoczi, G. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Knapp, S. | ||||||
![]() | ![]() Title: Activation Segment Dimerization: A Mechanism for Kinase Autophosphorylation of Non-Consensus Sites. Authors: Pike, A.C.W. / Rellos, P. / Niesen, F.H. / Turnbull, A. / Oliver, A.W. / Parker, S.A. / Turk, B.E. / Pearl, L.H. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.5 KB | Display | ![]() |
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PDB format | ![]() | 57.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.3 KB | Display | ![]() |
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Full document | ![]() | 796.2 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j51SC ![]() 2j7tC ![]() 2j90C ![]() 2jfmC ![]() 2uv2C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37322.031 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 19-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9H2G2, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 154 molecules ![](data/chem/img/DKI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DKI / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SCN / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | K25T MUTATION DUE TO CLONING ARTIFACT |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.1 % |
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Crystal grow | pH: 6.5 Details: 18% PEG3350,10% ETHYLENE GLYCOL, 0.15 KSCN, 0.1M BISTRIS PROPANE PH6.5, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49 Å / Num. obs: 27969 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2J51 Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.975 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PHOSPHO GROUPS ON THR183 AND SER189 HAVE BEEN MODELLED WITH OCCUPANCIES OF 0.7 AND 0.3 RESPECTIVELY. MASS SPEC INDICATES RATIO OF MONO-TO- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PHOSPHO GROUPS ON THR183 AND SER189 HAVE BEEN MODELLED WITH OCCUPANCIES OF 0.7 AND 0.3 RESPECTIVELY. MASS SPEC INDICATES RATIO OF MONO-TO-DI PHOSPHORYLATION IS 70- 30
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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