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- PDB-5ko1: Pseudokinase Domain of MLKL bound to Compound 4. -

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Basic information

Entry
Database: PDB / ID: 5ko1
TitlePseudokinase Domain of MLKL bound to Compound 4.
ComponentsMixed lineage kinase domain-like protein
KeywordsMEMBRANE PROTEINS/INHIBITOR / Pseudokinase domain MLKL Type1 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 / necroptotic process / protein homotrimerization / 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 / necroptotic process / protein homotrimerization / 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
: / : / Mixed lineage kinase domain-like N-terminal domain / Adaptor protein Cbl, N-terminal domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...: / : / Mixed lineage kinase domain-like N-terminal domain / Adaptor protein Cbl, N-terminal domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-6UY / Mixed lineage kinase domain-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsMarcotte, D.J.
CitationJournal: 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
DepositionJun 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Data collection / Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6002
Polymers32,2331
Non-polymers3661
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.400, 74.880, 127.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Mixed lineage kinase domain-like protein / hMLKL


Mass: 32233.166 Da / Num. of mol.: 1 / 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 ChemComp-6UY / [(1~{R})-2-[(4-fluorophenyl)amino]-2-oxidanylidene-1-phenyl-ethyl] 3-azanylpyrazine-2-carboxylate


Mass: 366.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15FN4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M BisTRIS pH 6.5 20% PEG3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.16→63.53 Å / Num. obs: 18649 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.058 / Rrim(I) all: 0.155 / Net I/σ(I): 10 / Num. measured all: 131173 / Scaling rejects: 80
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.16-2.237.10.7331117315780.6760.2940.7912.7100
8.91-63.535.80.06317473020.9920.0290.06921.697.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALAdata scaling
PDB_EXTRACT3.2data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WMI

4wmi


Resolution: 2.16→63.53 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.554 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 934 5 %RANDOM
Rwork0.1877 ---
obs0.1896 17685 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.49 Å2 / Biso mean: 32.069 Å2 / Biso min: 14.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.16→63.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 27 131 2288
Biso mean--33.51 37.9 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192226
X-RAY DIFFRACTIONr_bond_other_d0.0020.022181
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9973002
X-RAY DIFFRACTIONr_angle_other_deg1.1033.0055029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95723.762101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70215420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6831518
X-RAY DIFFRACTIONr_chiral_restr0.1150.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212472
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02502
X-RAY DIFFRACTIONr_mcbond_it2.7122.9481070
X-RAY DIFFRACTIONr_mcbond_other2.7072.9431069
X-RAY DIFFRACTIONr_mcangle_it4.0674.4011338
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 67 -
Rwork0.265 1273 -
all-1340 -
obs--99.93 %

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