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- PDB-8a5j: Crystal structure of Human STE20-like kinase 1, MST1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 8a5j
TitleCrystal structure of Human STE20-like kinase 1, MST1 in complex with compound XMU-MP-1
ComponentsSerine/threonine-protein kinase 4 37kDa subunit
KeywordsTRANSFERASE / serine-threonine kinase / autophosphorylation / MST1
Function / homology
Function and homology information


positive regulation of hepatocyte apoptotic process / cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth / hippo signaling ...positive regulation of hepatocyte apoptotic process / cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate-dependent cell migration, cell attachment to substrate / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / organ growth / branching involved in blood vessel morphogenesis / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / keratinocyte differentiation / protein serine/threonine kinase activator activity / epithelial cell proliferation / central nervous system development / protein tetramerization / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / protein import into nucleus / negative regulation of epithelial cell proliferation / positive regulation of protein binding / positive regulation of peptidyl-serine phosphorylation / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / protein autophosphorylation / nuclear body / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / magnesium ion binding / signal transduction / protein homodimerization activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53-like tetramerisation domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / p53-like tetramerisation domain superfamily / 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
Similarity search - Domain/homology
Chem-5BS / Serine/threonine-protein kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.123 Å
AuthorsNawrotek, A. / Vuillard, L. / Miallau, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the Kelch domain of human Keap1in complex with ligand S217879
Authors: Weber, C. / Vuillard, L. / Delerive, P. / Miallau, L.
History
DepositionJun 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 4 37kDa subunit
B: Serine/threonine-protein kinase 4 37kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8604
Polymers64,0272
Non-polymers8332
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-7 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.41, 111.41, 170.655
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Serine/threonine-protein kinase 4 37kDa subunit / MST1/N


Mass: 32013.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TPO= phosphorylated threonine / Source: (gene. exp.) Homo sapiens (human) / Gene: STK4, KRS2, MST1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13043
#2: Chemical ChemComp-5BS / 4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide


Mass: 416.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16N6O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.39 Å3/Da / Density % sol: 72.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium citrate pH 7.0, 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.125→93.29 Å / Num. obs: 52591 / % possible obs: 86.1 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.033 / Net I/σ(I): 20.2
Reflection shellResolution: 2.125→2.263 Å / Num. unique obs: 2632 / CC1/2: 0.654

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.123→93.29 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.159
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 2753 -RANDOM
Rwork0.2427 ---
obs0.243 52599 85.8 %-
Displacement parametersBiso mean: 62.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.1938 Å20 Å20 Å2
2--0.1938 Å20 Å2
3----0.3876 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.123→93.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 56 81 4328
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094382HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.985954HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1554SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes779HARMONIC5
X-RAY DIFFRACTIONt_it4382HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion591SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3428SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion17.01
LS refinement shellResolution: 2.123→2.22 Å
RfactorNum. reflection% reflection
Rfree0.3596 57 -
Rwork0.3122 --
obs--14.24 %

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