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- PDB-5knj: Pseudokinase Domain of MLKL bound to Compound 1. -

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Basic information

Entry
Database: PDB / ID: 5knj
TitlePseudokinase Domain of MLKL bound to Compound 1.
ComponentsMixed lineage kinase domain-like protein
KeywordsMEMBRANE 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
: / : / 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-6UX / Mixed lineage kinase domain-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 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 28, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6134
Polymers64,4662
Non-polymers1,1472
Water1,964109
1
A: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8072
Polymers32,2331
Non-polymers5741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8072
Polymers32,2331
Non-polymers5741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.488, 90.879, 115.618
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / 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: _ / Auth seq-ID: 193 - 468 / Label seq-ID: 5 - 280

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


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 ChemComp-6UX / 1-[4-[methyl-[2-[(3-sulfamoylphenyl)amino]pyrimidin-4-yl]amino]phenyl]-3-[4-(trifluoromethyloxy)phenyl]urea


Mass: 573.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H22F3N7O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Na Citrate and 15% 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: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 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: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.88-3.047.10.8681390919560.8210.3480.9362.5100
9.11-49.296.20.07630254900.9940.0330.08419.699.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimlessdata scaling
PDB_EXTRACT3.2data extraction
MOLREPphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MWI

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 674 5 %RANDOM
Rwork0.1925 ---
obs0.1955 12882 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.21 Å2 / Biso mean: 46.866 Å2 / Biso min: 20.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0 Å2
2--0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2.88→71.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 80 109 4189
Biso mean--39.3 46.35 -
Num. residues----511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194170
X-RAY DIFFRACTIONr_bond_other_d0.0020.023997
X-RAY DIFFRACTIONr_angle_refined_deg1.6862.0025639
X-RAY DIFFRACTIONr_angle_other_deg1.9123.0089183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.66123.966174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50915735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.041527
X-RAY DIFFRACTIONr_chiral_restr0.1130.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214592
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02909
X-RAY DIFFRACTIONr_mcbond_it3.2444.7062041
X-RAY DIFFRACTIONr_mcbond_other3.2434.7062042
X-RAY DIFFRACTIONr_mcangle_it5.267.0512542
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

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.88→2.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 42 -
Rwork0.317 946 -
all-988 -
obs--100 %

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