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- PDB-2j90: Crystal structure of human ZIP kinase in complex with a tetracycl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j90 | ||||||
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Title | Crystal structure of human ZIP kinase in complex with a tetracyclic pyridone inhibitor (Pyridone 6) | ||||||
![]() | DEATH-ASSOCIATED PROTEIN KINASE 3 | ||||||
![]() | TRANSFERASE / NUCLEAR PROTEIN / NUCLEOTIDE-BINDING / SERINE/THREONINE- PROTEIN KINASE / CHROMATIN REGULATOR / MYOSIN PHOSPHORYLATION / KINASE / MUSCLE / APOPTOSIS / ATP-BINDING | ||||||
Function / homology | ![]() regulation of myosin II filament organization / leucine zipper domain binding / cAMP response element binding protein binding / regulation of smooth muscle contraction / Caspase activation via Dependence Receptors in the absence of ligand / regulation of cell motility / regulation of focal adhesion assembly / regulation of mitotic nuclear division / regulation of mitotic cell cycle / regulation of autophagy ...regulation of myosin II filament organization / leucine zipper domain binding / cAMP response element binding protein binding / regulation of smooth muscle contraction / Caspase activation via Dependence Receptors in the absence of ligand / regulation of cell motility / regulation of focal adhesion assembly / regulation of mitotic nuclear division / regulation of mitotic cell cycle / regulation of autophagy / regulation of actin cytoskeleton organization / apoptotic signaling pathway / PML body / small GTPase binding / cellular response to type II interferon / positive regulation of canonical Wnt signaling pathway / chromatin organization / regulation of cell shape / regulation of apoptotic process / protein autophosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of cell migration / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / regulation of DNA-templated transcription / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Turnbull, A.P. / Berridge, G. / Fedorov, O. / Pike, A.C.W. / Savitsky, P. / Eswaran, J. / Papagrigoriou, E. / Ugochukwa, E. / von Delft, F. / Gileadi, O. ...Turnbull, A.P. / Berridge, G. / Fedorov, O. / Pike, A.C.W. / Savitsky, P. / Eswaran, J. / Papagrigoriou, E. / Ugochukwa, E. / von Delft, F. / Gileadi, O. / 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 | ![]() | 130.5 KB | Display | ![]() |
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PDB format | ![]() | 100.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j51C ![]() 2j7tC ![]() 2jflC ![]() 2jfmC ![]() 2uv2C ![]() 1jksS ![]() 1jktS ![]() 1wvxS ![]() 1yrpS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.92836, -0.31836, -0.19183), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35176.742 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 9-289 Source method: isolated from a genetically manipulated source Details: DIPHOSPHORYLATED FORM (SER50 AND THR265) / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O43293, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 335 molecules ![](data/chem/img/IZA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | pH: 8 / Details: 30% PEG 1000 0.1M SPG BUFFER PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 23, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 48089 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.201 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 30.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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