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- PDB-4c34: PKA-S6K1 Chimera with Staurosporine bound -

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Basic information

Entry
Database: PDB / ID: 4c34
TitlePKA-S6K1 Chimera with Staurosporine bound
Components(CAMP-DEPENDENT PROTEIN KINASE ...Protein kinase A) x 2
KeywordsTRANSFERASE/INHIBITOR / TRANSFERASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / protein kinase A signaling / negative regulation of TORC1 signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
N-OCTANOYL-N-METHYLGLUCAMINE / STAUROSPORINE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsCouty, S. / Westwood, I.M. / Kalusa, A. / Cano, C. / Travers, J. / Boxall, K. / Chow, C.L. / Burns, S. / Schmitt, J. / Pickard, L. ...Couty, S. / Westwood, I.M. / Kalusa, A. / Cano, C. / Travers, J. / Boxall, K. / Chow, C.L. / Burns, S. / Schmitt, J. / Pickard, L. / Barillari, C. / McAndrew, P.C. / Clarke, P.A. / Linardopoulos, S. / Griffin, R.J. / Aherne, G.W. / Raynaud, F.I. / Workman, P. / Jones, K. / van Montfort, R.L.M.
CitationJournal: Oncotarget / Year: 2013
Title: The discovery of potent ribosomal S6 kinase inhibitors by high-throughput screening and structure-guided drug design.
Authors: Couty, S. / Westwood, I.M. / Kalusa, A. / Cano, C. / Travers, J. / Boxall, K. / Chow, C.L. / Burns, S. / Schmitt, J. / Pickard, L. / Barillari, C. / McAndrew, P.C. / Clarke, P.A. / ...Authors: Couty, S. / Westwood, I.M. / Kalusa, A. / Cano, C. / Travers, J. / Boxall, K. / Chow, C.L. / Burns, S. / Schmitt, J. / Pickard, L. / Barillari, C. / McAndrew, P.C. / Clarke, P.A. / Linardopoulos, S. / Griffin, R.J. / Aherne, G.W. / Raynaud, F.I. / Workman, P. / Jones, K. / van Montfort, R.L.
History
DepositionAug 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: citation / citation_author ...citation / citation_author / pdbx_database_status / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 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 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
I: CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8825
Polymers43,0022
Non-polymers8803
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-3.7 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.430, 72.710, 77.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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CAMP-DEPENDENT PROTEIN KINASE ... , 2 types, 2 molecules AI

#1: Protein CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA / CAMP-dependent pathway / PKA C-ALPHA


Mass: 41028.641 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PKA-S6K1 CHIMERA / Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00517, cAMP-dependent protein kinase
#2: Protein/peptide CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA / CAMP-dependent pathway / PKI-ALPHA


Mass: 1973.177 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-23 / Source method: obtained synthetically / Source: (synth.) BOS TAURUS (cattle) / References: UniProt: Q3SX13

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Non-polymers , 4 types, 382 molecules

#3: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG8 / N-OCTANOYL-N-METHYLGLUCAMINE / MEGA 8 / N-(D-GLUCITYL)-N-METHYLOCTANAMIDE


Mass: 321.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H31NO6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPKA-S6K1 CHIMERA MUTATIONS ARE F54Y, M120L, V123L, L173M AND Q181K

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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: 2.45 Å3/Da / Density % sol: 49.9 % / Description: NONE
Crystal growpH: 6.4
Details: 18 MG/ML PROTEIN IN 25MM MES-BIS-TRIS PH 6.5, 75MM LICL, 0.1MM EDTA, 1MM MEGA-8, 1MM DTT AND 1MM PKI PEPTIDE MIXED 1:1 WITH 8-16% AQUEOUS METHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→42.08 Å / Num. obs: 37804 / % possible obs: 99.6 % / Observed criterion σ(I): 1.5 / Redundancy: 3.3 % / Biso Wilson estimate: 24.05 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.9
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C33

4c33


Resolution: 1.78→36.35 Å / Cor.coef. Fo:Fc: 0.9544 / Cor.coef. Fo:Fc free: 0.9347 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.125 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 1906 5.05 %RANDOM
Rwork0.1778 ---
obs0.1796 37753 99.19 %-
Displacement parametersBiso mean: 26.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.3308 Å20 Å20 Å2
2--1.8677 Å20 Å2
3----1.5369 Å2
Refine analyzeLuzzati coordinate error obs: 0.214 Å
Refinement stepCycle: LAST / Resolution: 1.78→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2880 0 48 379 3307
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013025HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.964109HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1024SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes474HARMONIC5
X-RAY DIFFRACTIONt_it3025HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion16.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion375SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3933SEMIHARMONIC4
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2573 135 4.85 %
Rwork0.22 2649 -
all0.2217 2784 -
obs--99.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.79920.02690.22621.0181-0.09350.7725-0.1496-0.0660.5429-0.04660.01620.4792-0.4294-0.18970.13340.10630.095-0.1305-0.1164-0.04240.4723-9.833617.5145-15.8733
20.350.461-0.23872.34570.15220.79030.0369-0.03470.0884-0.0044-0.0423-0.1038-0.18320.01680.0055-0.03180.0152-0.0362-0.1650.00760.08145.03998.95-21.4656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN I

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