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- PDB-6zz1: Crystal structure of MLKL executioner domain in complex with a co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zz1 | ||||||
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Title | Crystal structure of MLKL executioner domain in complex with a covalent inhibitor | ||||||
![]() | Mixed lineage kinase domain-like protein | ||||||
![]() | LIPID BINDING PROTEIN / Necroptosis | ||||||
Function / homology | ![]() execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / TRP channels / RIPK1-mediated regulated necrosis / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus ...execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / TRP channels / RIPK1-mediated regulated necrosis / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus / cell surface receptor signaling pathway / protein-containing complex binding / protein kinase binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fiegen, D. / Bauer, M. / Nar, H. | ||||||
![]() | ![]() Title: Locking mixed-lineage kinase domain-like protein in its auto-inhibited state prevents necroptosis. Authors: Rubbelke, M. / Fiegen, D. / Bauer, M. / Binder, F. / Hamilton, J. / King, J. / Thamm, S. / Nar, H. / Zeeb, 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 | ![]() | 138 KB | Display | ![]() |
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PDB format | ![]() | 108.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zleC ![]() 6zprC ![]() 6zvoC ![]() 4btfS C: citing same article ( 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17642.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 32 % Polyethylene glycol monomethyl ether 2,000, 0.15 M Potassium bromide, 0.1 M TRIS, pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99994 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→19.705 Å / Num. obs: 28984 / % possible obs: 82.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.029 / Rsym value: 0.029 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.64→1.746 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1449 / Rsym value: 0.797 / % possible all: 24.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4btf Resolution: 1.64→20.05 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.119
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Displacement parameters | Biso mean: 52.09 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→20.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.7 Å
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