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Open data
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Basic information
Entry | Database: PDB / ID: 2cke | ||||||
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Title | Human death-associated DRP-1 kinase in complex with inhibitor | ||||||
![]() | DEATH-ASSOCIATED PROTEIN KINASE 2 | ||||||
![]() | TRANSFERASE/INHIBITOR / TRANSFERASE-INHIBITOR COMPLEX / CALMODULIN-BINDING / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / APOPTOSIS | ||||||
Function / homology | ![]() positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of neutrophil chemotaxis / anoikis / regulation of autophagy / cytoplasmic vesicle / regulation of apoptotic process / protein autophosphorylation ...positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of neutrophil chemotaxis / anoikis / regulation of autophagy / cytoplasmic vesicle / regulation of apoptotic process / protein autophosphorylation / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kursula, P. / Wilmanns, M. | ||||||
![]() | ![]() Title: Crystal Structure of Human Drp-1 Complexed with an Inhibitor Authors: Kursula, P. / 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 | ![]() | 245.7 KB | Display | ![]() |
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PDB format | ![]() | 198.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2a2aS S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 37166.504 Da / Num. of mol.: 4 / Fragment: RESIDUES 11-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UIK4, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-IQU / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.48 % |
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Crystal grow | pH: 8.5 Details: 0.2 M LI SULFATE, 0.1 M TRIS PH 8.5, 25 % PEG 4000, 15 % GLYCEROL, 10 MM DTT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.814 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 30010 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.8 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2A2A Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.893 / SU B: 37.206 / SU ML: 0.341 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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