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- PDB-4qmx: MST3 in complex with SARACATINIB -

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Basic information

Entry
Database: PDB / ID: 4qmx
TitleMST3 in complex with SARACATINIB
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-H8H / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.882 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 / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.5Oct 9, 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)35,5662
Polymers35,0241
Non-polymers5421
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.551, 55.119, 60.640
Angle α, β, γ (deg.)90.00, 111.58, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer per ASU

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE 24 / STE20-LIKE KINASE MST3 / MST-3 / MAMMALIAN STE20-LIKE PROTEIN KINASE 3


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: STK24, MST3, 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-H8H / N-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE / SARACATINIB


Mass: 542.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H32ClN5O5 / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.5 mg/mL MST3, 1 mM SARACATINIB,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: Nov 6, 2012 / 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: 1.9→20 Å / Num. obs: 22568 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.047 / Net I/σ(I): 42.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 8.76 / Rsym value: 0.233 / % possible all: 95.9

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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: pdb entry 3CKW

3ckw


Resolution: 1.882→34.492 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1151 4.98 %
Rwork0.1794 --
obs-21430 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.882→34.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 38 163 2507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072397
X-RAY DIFFRACTIONf_angle_d1.0913241
X-RAY DIFFRACTIONf_dihedral_angle_d16.578918
X-RAY DIFFRACTIONf_chiral_restr0.043355
X-RAY DIFFRACTIONf_plane_restr0.005406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8823-1.96790.2971390.22272613X-RAY DIFFRACTION93
1.9679-2.07170.26581320.19092682X-RAY DIFFRACTION96
2.0717-2.20150.21061440.18042706X-RAY DIFFRACTION97
2.2015-2.37140.22511490.18382717X-RAY DIFFRACTION97
2.3714-2.610.22591400.20052765X-RAY DIFFRACTION98
2.61-2.98750.25531470.2022757X-RAY DIFFRACTION98
2.9875-3.76320.2011500.17912812X-RAY DIFFRACTION99
3.7632-34.49740.19161500.15092889X-RAY DIFFRACTION100

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