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Yorodumi- PDB-3zxt: Dimeric structure of DAPK-1 catalytic domain in complex with AMPP... -
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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 | ||||||
Components | DEATH-ASSOCIATED PROTEIN KINASE 1DAPK1 | ||||||
Keywords | TRANSFERASE / APOPTOSIS / ATP BINDING | ||||||
Function / homology | Function and homology information 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 / calmodulin-dependent protein kinase activity / syntaxin-1 binding / regulation of NMDA receptor 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 / calmodulin-dependent protein kinase activity / syntaxin-1 binding / regulation of NMDA receptor 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 / negative regulation of translation / postsynaptic density / protein autophosphorylation / calmodulin binding / 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 / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | de Diego, I. / Lehmann, F. / Wilmanns, M. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zxt.cif.gz | 401.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zxt.ent.gz | 328.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/3zxt ftp://data.pdbj.org/pub/pdb/validation_reports/zx/3zxt | HTTPS FTP |
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-Related structure data
Related structure data | 2y4pC 2y4vC 2w4jS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9235 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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