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- PDB-7nm2: Solution structure of MLKL executioner domain in complex with a f... -

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Basic information

Entry
Database: PDB / ID: 7nm2
TitleSolution structure of MLKL executioner domain in complex with a fragment
ComponentsMixed lineage kinase domain-like protein
KeywordsLIPID BINDING PROTEIN / Necroptosis
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 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-UJ5 / Mixed lineage kinase domain-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRuebbelke, M. / Bauer, M. / Hamilton, J. / Binder, F. / Nar, H. / Zeeb, M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery and Structure-Based Optimization of Fragments Binding the Mixed Lineage Kinase Domain-like Protein Executioner Domain.
Authors: Rubbelke, M. / Hamilton, J. / Binder, F. / Bauer, M. / King, J. / Nar, H. / Zeeb, M.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 24, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,5092
Polymers18,1851
Non-polymers3241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9940 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

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


Mass: 18184.961 Da / Num. of mol.: 1
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-UJ5 / 2-[(~{S})-methoxy-(4-propan-2-ylphenyl)methyl]-3~{H}-benzimidazole-5-carboxylic acid


Mass: 324.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
213isotropic12D 1H-15N HSQC
223isotropic13D HN(CA)CB
233isotropic13D HNccH TOCSY
243isotropic13D HNCC TOCSY
253isotropic13D 1H-15N NOESY
1102isotropic12D 1H-13C HSQC aliphatic
192isotropic12D 1H-13C HSQC aromatic
182isotropic13D (H)CCH-TOCSY
172isotropic13D (H)CCH-TOCSY
162isotropic13D 1H-13C NOESY aliphatic
1112isotropic13D 1H-13C NOESY aromatic
1122isotropic13D filt. 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution2430 uM [U-13C; U-15N] MLKL executioner domain, 700 uM Cpd 5, 100% D2Oin D2O100% D2O
solution3400 uM [U-13C; U-15N] MLKL executioner domain, 700 uM Cpd 5, 93% H2O/7% D2Oin H2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
430 uMMLKL executioner domain[U-13C; U-15N]2
700 uMCpd 5natural abundance2
400 uMMLKL executioner domain[U-13C; U-15N]3
700 uMCpd 5natural abundance3
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
120 mM sodium phosphate, 150 mM sodium chloride, 5 mM DTT170 mMin D2O7.11 atm298 K
220 mM sodium phosphate, 150 mM sodium chloride, 5 mM DTT170 mMin H2O7.51 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.9Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
TopSpin3.5Bruker Biospinprocessing
TopSpin3.6Bruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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