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- PDB-4qms: MST3 in complex with DASATINIB -

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Basic information

Entry
Database: PDB / ID: 4qms
TitleMST3 in complex with DASATINIB
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 / Apoptotic cleavage of cellular proteins / negative regulation of cell migration / cellular response to starvation / protein autophosphorylation / 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 / Apoptotic cleavage of cellular proteins / negative regulation of cell migration / cellular response to starvation / protein autophosphorylation / cellular response to oxidative stress / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-1N1 / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.883 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 1.1Jul 13, 2016Group: Database references
Revision 1.2Apr 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 1.3Sep 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)35,6094
Polymers35,0241
Non-polymers5863
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.486, 55.133, 60.236
Angle α, β, γ (deg.)90.00, 111.35, 90.00
Int Tables number4
Space group name H-MP1211

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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: unp 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-1N1 / N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE / Dasatinib


Mass: 488.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26ClN7O2S / Comment: medication*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.5 mg/mL MST3, 1 mM DASATINIB, 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 / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 20, 2013 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541781
21.541
ReflectionResolution: 1.88→20 Å / Num. obs: 23554 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.078 / Net I/σ(I): 47.5
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 14.1 / Rsym value: 0.143 / % possible all: 85.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CKW

3ckw


Resolution: 1.883→34.499 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1166 4.96 %
Rwork0.169 --
obs-23527 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.883→34.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 38 170 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072374
X-RAY DIFFRACTIONf_angle_d1.1513211
X-RAY DIFFRACTIONf_dihedral_angle_d14.261916
X-RAY DIFFRACTIONf_chiral_restr0.046353
X-RAY DIFFRACTIONf_plane_restr0.005405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8826-1.96820.23091400.18322706X-RAY DIFFRACTION96
1.9682-2.0720.20481500.15812782X-RAY DIFFRACTION99
2.072-2.20180.17431480.15262785X-RAY DIFFRACTION100
2.2018-2.37180.20061400.16472788X-RAY DIFFRACTION99
2.3718-2.61040.22171510.1882809X-RAY DIFFRACTION100
2.6104-2.98790.28021410.18982793X-RAY DIFFRACTION99
2.9879-3.76370.21671450.17392819X-RAY DIFFRACTION99
3.7637-34.50470.19331510.15352879X-RAY DIFFRACTION99

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