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- PDB-4qmp: MST3 IN COMPLEX WITH CDK1/2 INHIBITOR III, 5-AMINO-3-{[4-(AMINOSU... -

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Basic information

Entry
Database: PDB / ID: 4qmp
TitleMST3 IN COMPLEX WITH CDK1/2 INHIBITOR III, 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE
ComponentsSerine/threonine-protein kinase 24
KeywordsTransferase/transferase inhibitor / PROTEIN KINASE / MST3 / STK24 / STERILE 20-LIKE KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / SERINE/THREONINE-TRANSFERASE / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


Apoptotic execution phase / FAR/SIN/STRIPAK complex / regulation of axon regeneration / intrinsic apoptotic signaling pathway in response to oxidative stress / execution phase of apoptosis / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cellular response to oxidative stress ...Apoptotic execution phase / FAR/SIN/STRIPAK complex / regulation of axon regeneration / intrinsic apoptotic signaling pathway in response to oxidative stress / execution phase of apoptosis / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cellular response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / protein phosphorylation / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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-DKI / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOlesen, S.H. / Watts, C. / Zhu, J.-Y. / Schonbrunn, E.
CitationJournal: Chemmedchem / Year: 2016
Title: Discovery of Diverse Small-Molecule Inhibitors of Mammalian Sterile20-like Kinase 3 (MST3).
Authors: Olesen, S.H. / Zhu, J.Y. / Martin, M.P. / Schonbrunn, E.
History
DepositionJun 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Apr 11, 2018Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _diffrn_source.pdbx_synchrotron_beamline ..._chem_comp.name / _diffrn_source.pdbx_synchrotron_beamline / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5113
Polymers35,0241
Non-polymers4882
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.440, 57.450, 61.540
Angle α, β, γ (deg.)90.00, 93.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-587-

HOH

21A-637-

HOH

Detailsmonomer per ASU

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Components

#1: Protein Serine/threonine-protein kinase 24 / Mammalian STE20-like protein kinase 3 / MST-3 / STE20-like kinase MST3 / Serine/threonine-protein ...Mammalian STE20-like protein kinase 3 / MST-3 / STE20-like kinase MST3 / Serine/threonine-protein kinase 24 36 kDa subunit / Mammalian STE20-like protein kinase 3 N-terminal / MST3/N / Serine/threonine-protein kinase 24 12 kDa subunit / Mammalian STE20-like protein kinase 3 C-terminal / MST3/C


Mass: 35023.934 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MST3, STK24, STK3 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DKI / 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE / CDK 1/2 INHIBITOR


Mass: 425.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13F2N7O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED SEQUENCE REFERS TO THE ISOFORM A

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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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 12.5 mg/mL MST3, 1 mM CDK2 Inhibitor III, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 28, 2012 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 23474 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.039 / Net I/σ(I): 21.72
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.76 / Rsym value: 0.366 / % possible all: 99.8

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CKW

3ckw


Resolution: 2→19.631 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 1174 5 %
Rwork0.1769 --
obs-23472 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 32 185 2536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082401
X-RAY DIFFRACTIONf_angle_d1.0753247
X-RAY DIFFRACTIONf_dihedral_angle_d18.398927
X-RAY DIFFRACTIONf_chiral_restr0.042356
X-RAY DIFFRACTIONf_plane_restr0.005411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.09090.26321450.20682756X-RAY DIFFRACTION100
2.0909-2.2010.25111470.20712800X-RAY DIFFRACTION100
2.201-2.33870.26611450.20612758X-RAY DIFFRACTION100
2.3387-2.5190.26051460.20832761X-RAY DIFFRACTION100
2.519-2.77180.27451470.21732794X-RAY DIFFRACTION100
2.7718-3.17150.25621470.20352797X-RAY DIFFRACTION100
3.1715-3.99020.21081470.1642788X-RAY DIFFRACTION100
3.9902-19.63240.18561500.13762844X-RAY DIFFRACTION99

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