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- PDB-5d9l: Rsk2 N-terminal Kinase in Complex with bis-phenol pyrazole -

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Basic information

Entry
Database: PDB / ID: 5d9l
TitleRsk2 N-terminal Kinase in Complex with bis-phenol pyrazole
ComponentsRibosomal protein S6 kinase alpha-3Ribosome
KeywordsTRANSFERASE/TRANSFERASE inhibitor / kinase / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / toll-like receptor signaling pathway / Recycling pathway of L1 / ERK/MAPK targets / cysteine-type endopeptidase inhibitor activity involved in apoptotic process ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / toll-like receptor signaling pathway / Recycling pathway of L1 / ERK/MAPK targets / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / central nervous system development / skeletal system development / positive regulation of cell differentiation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Senescence-Associated Secretory Phenotype (SASP) / chemical synaptic transmission / positive regulation of cell growth / peptidyl-serine phosphorylation / response to lipopolysaccharide / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / synapse / nucleolus / negative regulation of apoptotic process / protein kinase binding / magnesium ion binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
Similarity search - Domain/homology
4,4'-(1H-pyrazole-3,4-diyl)diphenol / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsAppleton, B.A.
Citation
Journal: J.Med.Chem. / Year: 2015
Title: Discovery of Potent and Selective RSK Inhibitors as Biological Probes.
Authors: Jain, R. / Mathur, M. / Lan, J. / Costales, A. / Atallah, G. / Ramurthy, S. / Subramanian, S. / Setti, L. / Feucht, P. / Warne, B. / Doyle, L. / Basham, S. / Jefferson, A.B. / Lindvall, M. / ...Authors: Jain, R. / Mathur, M. / Lan, J. / Costales, A. / Atallah, G. / Ramurthy, S. / Subramanian, S. / Setti, L. / Feucht, P. / Warne, B. / Doyle, L. / Basham, S. / Jefferson, A.B. / Lindvall, M. / Appleton, B.A. / Shafer, C.M.
#1: Journal: Mol Cancer Res. / Year: 2014
Title: Novel potent and selective inhibitors of p90 ribosomal S6 kinase reveal the heterogeneity of RSK function in MAPK-driven cancers.
Authors: Aronchik, I. / Appleton, B.A. / Basham, S.E. / Crawford, K. / Del Rosario, M. / Doyle, L.V. / Estacio, W.F. / Lan, J. / Lindvall, M.K. / Luu, C.A. / Ornelas, E. / Venetsanakos, E. / Shafer, ...Authors: Aronchik, I. / Appleton, B.A. / Basham, S.E. / Crawford, K. / Del Rosario, M. / Doyle, L.V. / Estacio, W.F. / Lan, J. / Lindvall, M.K. / Luu, C.A. / Ornelas, E. / Venetsanakos, E. / Shafer, C.M. / Jefferson, A.B.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5493
Polymers37,2051
Non-polymers3442
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.450, 58.590, 78.570
Angle α, β, γ (deg.)90.000, 100.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosomal protein S6 kinase alpha-3 / Ribosome / S6K-alpha-3 / 90 kDa ribosomal protein S6 kinase 3 / p90RSK3 / Insulin-stimulated protein kinase 1 ...S6K-alpha-3 / 90 kDa ribosomal protein S6 kinase 3 / p90RSK3 / Insulin-stimulated protein kinase 1 / ISPK-1 / MAP kinase-activated protein kinase 1b / MAPKAPK-1b / Ribosomal S6 kinase 2 / RSK-2 / pp90RSK2


Mass: 37204.988 Da / Num. of mol.: 1 / Fragment: N-terminal kinase (UNP residues 39-359)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA3, ISPK1, MAPKAPK1B, RSK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P51812, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-583 / 4,4'-(1H-pyrazole-3,4-diyl)diphenol


Mass: 252.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12N2O2
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2 M lithium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→46.68 Å / Num. obs: 16295 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.85 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.111 / Net I/σ(I): 7.9 / Num. measured all: 59944
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 99.7

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
2.15-2.413.70.6162.61699846130.6790.372
4.82-46.683.60.05518.4532714980.9970.034

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
BUSTER-TNTBUSTER 2.11.4refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→46.68 Å / Cor.coef. Fo:Fc: 0.9345 / Cor.coef. Fo:Fc free: 0.8853 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.242 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.193
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 812 4.99 %RANDOM
Rwork0.1651 ---
obs0.168 16281 99.27 %-
Displacement parametersBiso max: 99.34 Å2 / Biso mean: 20.39 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-4.1348 Å20 Å20.3287 Å2
2--0.0517 Å20 Å2
3----4.1865 Å2
Refine analyzeLuzzati coordinate error obs: 0.216 Å
Refinement stepCycle: final / Resolution: 2.15→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 25 165 2599
Biso mean--17.92 24.96 -
Num. residues----299
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d884SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes380HARMONIC5
X-RAY DIFFRACTIONt_it2495HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion309SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2975SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2495HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3362HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion16.69
LS refinement shellResolution: 2.15→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2611 147 5.16 %
Rwork0.1888 2704 -
all0.1926 2851 -
obs--99.27 %
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)
10.76520.2661-0.36040.6556-0.33510.4820.0208-0.0643-0.0609-0.0042-0.0393-0.0428-0.03320.04330.0185-0.0013-0.0009-0.0184-0.01650.0085-0.04291.1842.32434.024
20.2442-0.22520.11830.86580.12990.9405-0.02340.0309-0.0614-0.0608-0.00880.02510.03-0.01670.0322-0.023-0.0037-0.0097-0.0317-0.0106-0.0299.86810.55410.854
30.5548-0.1746-0.36870.2598-0.11560.39330.00180.01010.0143-0.00380.0065-0.0058-0.0067-0.0078-0.00830.04050.03380.0255-0.0734-0.0630.022-3.05533.49433.105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|49 - A|151 }A49 - 151
2X-RAY DIFFRACTION2{ A|152 - A|348 }A152 - 348
3X-RAY DIFFRACTION3{ A|349 - A|359 }A349 - 359

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