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- PDB-4qmm: MST3 IN COMPLEX WITH AT-9283, 4-[(2-{4-[(CYCLOPROPYLCARBAMOYL)AMI... -

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Basic information

Entry
Database: PDB / ID: 4qmm
TitleMST3 IN COMPLEX WITH AT-9283, 4-[(2-{4-[(CYCLOPROPYLCARBAMOYL)AMINO]-1H-PYRAZOL-3-YL}-1H-BENZIMIDAZOL-6-YL)METHYL]MORPHOLIN-4-IUM
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-35R / ACETATE ION / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.852 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 1.3Sep 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

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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)35,6837
Polymers35,0241
Non-polymers6596
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.653, 58.636, 61.789
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

Detailsmonomer per ASU

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 192 molecules

#2: Chemical ChemComp-35R / 1-cyclopropyl-3-{3-[5-(morpholin-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl}urea


Mass: 381.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.5 mg/mL MST3, 1 mM AT-9283, 25 mM TRIS, 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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2014
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 29959 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.035 / Net I/σ(I): 41.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 4.58 / Rsym value: 0.188 / % possible all: 87.5

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Processing

Software
NameVersionClassification
SERGUIdata 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: 1.852→19.89 Å / SU ML: 0.16 / σ(F): 1.37 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 1996 6.66 %
Rwork0.1413 --
obs-29954 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.852→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 45 186 2541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062403
X-RAY DIFFRACTIONf_angle_d1.0213244
X-RAY DIFFRACTIONf_dihedral_angle_d15.007928
X-RAY DIFFRACTIONf_chiral_restr0.038356
X-RAY DIFFRACTIONf_plane_restr0.005410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8516-1.89790.24771160.14821715X-RAY DIFFRACTION86
1.8979-1.94910.24551290.1481967X-RAY DIFFRACTION97
1.9491-2.00640.23261540.1352011X-RAY DIFFRACTION100
2.0064-2.07110.22521510.1332005X-RAY DIFFRACTION100
2.0711-2.14510.20761500.13122013X-RAY DIFFRACTION100
2.1451-2.23080.21271500.13131990X-RAY DIFFRACTION100
2.2308-2.33220.22021340.12952019X-RAY DIFFRACTION100
2.3322-2.4550.19621400.13842015X-RAY DIFFRACTION100
2.455-2.60850.21861430.14412022X-RAY DIFFRACTION100
2.6085-2.80940.22831380.16732044X-RAY DIFFRACTION100
2.8094-3.09110.21211470.1712022X-RAY DIFFRACTION100
3.0911-3.53630.19421470.15832022X-RAY DIFFRACTION100
3.5363-4.44710.15791500.12672046X-RAY DIFFRACTION100
4.4471-19.89070.17731470.12492067X-RAY DIFFRACTION99

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