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- PDB-3ckx: Crystal structure of sterile 20-like kinase 3 (MST3, STK24) in co... -

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Basic information

Entry
Database: PDB / ID: 3ckx
TitleCrystal structure of sterile 20-like kinase 3 (MST3, STK24) in complex with staurosporine
ComponentsSerine/threonine-protein kinase 24
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC / PROTEIN KINASE / MST3 / STK24 / STERILE 20-LIKE KINASE / STAUROSPORINE / Alternative splicing / ATP-binding / Cytoplasm / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
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
STAUROSPORINE / Serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAntonysamy, S.S. / Burley, S.K. / Buchanan, S. / Chau, F. / Feil, I. / Wu, L. / Sauder, J.M. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of sterile 20-like kinase 3 (MST3, STK24) in complex with staurosporine.
Authors: Antonysamy, S.S. / Burley, S.K. / Buchanan, S. / Chau, F. / Feil, I. / Wu, L. / Sauder, J.M.
History
DepositionMar 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 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)35,1202
Polymers34,6531
Non-polymers4671
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.369, 54.766, 61.136
Angle α, β, γ (deg.)90.000, 114.690, 90.000
Int Tables number4
Space group name H-MP1211

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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: 34653.211 Da / Num. of mol.: 1 / Fragment: Residues 31-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK24, MST3, STK3 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE TARGETDB ID NYSGXRC-5632A PROVIDED BY AUTHORS FOR THIS PROTEIN DID NOT EXIST IN TARGET DATABASE ...THE TARGETDB ID NYSGXRC-5632A PROVIDED BY AUTHORS FOR THIS PROTEIN DID NOT EXIST IN TARGET DATABASE AT THE TIME OF DEPOSITION.

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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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8.5
Details: 22% PEG 4000, 100 mM Tris-HCl, 200 mM Sodium acetate, pH 8.5, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 9, 2001
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 7930

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CKW

3ckw


Resolution: 2.7→24.77 Å
RfactorNum. reflection
Rfree0.268 -
Rwork0.204 -
obs0.204 7930
Displacement parametersBiso mean: 56.855 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 35 26 2205

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