+Open data
-Basic information
Entry | Database: PDB / ID: 5knj | ||||||
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Title | Pseudokinase Domain of MLKL bound to Compound 1. | ||||||
Components | Mixed lineage kinase domain-like protein | ||||||
Keywords | MEMBRANE PROTEINS/INHIBITOR / Pseudokinase domain MLKL Compound 1 GFE Out Type 2 inhibitor / MEMBRANE PROTEINS-INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | ||||||
Authors | Marcotte, D.J. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: ATP-Competitive MLKL Binders Have No Functional Impact on Necroptosis. Authors: Ma, B. / Marcotte, D. / Paramasivam, M. / Michelsen, K. / Wang, T. / Bertolotti-Ciarlet, A. / Jones, J.H. / Moree, B. / Butko, M. / Salafsky, J. / Sun, X. / McKee, T. / Silvian, L.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5knj.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5knj.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 5knj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/5knj ftp://data.pdbj.org/pub/pdb/validation_reports/kn/5knj | HTTPS FTP |
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-Related structure data
Related structure data | 5ko1C 4mwiS C: citing same article (ref.) S: Starting model for refinement |
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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 domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 193 - 468 / Label seq-ID: 5 - 280
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-Components
#1: Protein | Mass: 32233.166 Da / Num. of mol.: 2 / Fragment: UNP residues 191-471 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MLKL / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NB16 #2: Chemical | #3: 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: 2.22 Å3/Da / Density % sol: 44.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Na Citrate and 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 7, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.88→49.29 Å / Num. obs: 13598 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.079 / Rrim(I) all: 0.213 / Net I/σ(I): 8.9 / Num. measured all: 98117 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MWI Resolution: 2.88→71.45 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.885 / SU B: 17.434 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 132.21 Å2 / Biso mean: 46.866 Å2 / Biso min: 20.37 Å2
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Refinement step | Cycle: final / Resolution: 2.88→71.45 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 15720 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.88→2.955 Å / Total num. of bins used: 20
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