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- PDB-3zxt: Dimeric structure of DAPK-1 catalytic domain in complex with AMPP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zxt | ||||||
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Title | Dimeric structure of DAPK-1 catalytic domain in complex with AMPPCP- Mg | ||||||
![]() | DEATH-ASSOCIATED PROTEIN KINASE 1 | ||||||
![]() | TRANSFERASE / APOPTOSIS / ATP BINDING | ||||||
Function / homology | ![]() cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / syntaxin-1 binding / calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / syntaxin-1 binding / calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / postsynaptic density / negative regulation of translation / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / GTP binding / negative regulation of apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | de Diego, I. / Lehmann, F. / Wilmanns, M. | ||||||
![]() | ![]() Title: A Journey Through the Dap Kinase Architecture Authors: De Diego, I. / Kuper, J. / Lehmann, F. / Wilmanns, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 401.5 KB | Display | ![]() |
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PDB format | ![]() | 328.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 41.8 KB | Display | |
Data in CIF | ![]() | 55.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y4pC ![]() 2y4vC ![]() 2w4jS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 32725.262 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P53355, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-ACP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.39 % / Description: NONE |
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Crystal grow | Details: 0.1 M HEPES PH7.0, 0.1M MGCL2, 15% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 5, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9235 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→45.71 Å / Num. obs: 39321 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2W4J Resolution: 2.65→106.83 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / SU B: 29.35 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R: 0.694 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.865 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→106.83 Å
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Refine LS restraints |
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