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- PDB-5d9k: Rsk2 N-terminal Kinase in Complex with BI-D1870 -

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Basic information

Entry
Database: PDB / ID: 5d9k
TitleRsk2 N-terminal Kinase in Complex with BI-D1870
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
Chem-584 / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 / 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
B: Ribosomal protein S6 kinase alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9296
Polymers75,9622
Non-polymers9674
Water1,856103
1
A: Ribosomal protein S6 kinase alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4643
Polymers37,9811
Non-polymers4842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosomal protein S6 kinase alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4643
Polymers37,9811
Non-polymers4842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.190, 53.710, 207.940
Angle α, β, γ (deg.)90.000, 91.750, 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: 37980.852 Da / Num. of mol.: 2 / Fragment: N-terminal kinase (UNP residues 39-366)
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-584 / (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one


Mass: 391.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23F2N5O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 20% PEG3350, 0.075 M lithium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→52.002 Å / Num. all: 23564 / Num. obs: 23564 / % possible obs: 94.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 47.94 Å2 / Rpim(I) all: 0.075 / Rrim(I) all: 0.152 / Rsym value: 0.131 / Net I/av σ(I): 4.661 / Net I/σ(I): 7 / Num. measured all: 85221
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.55-2.693.50.5152.51111231550.30.5152.587.6
2.69-2.853.40.3651.91049930830.2170.3653.289.9
2.85-3.053.30.24231001029970.1460.2424.393.4
3.05-3.293.30.1784.1914628000.1070.1785.394.8
3.29-3.613.30.1245.6886127240.0760.1247.497.5
3.61-4.033.40.0996.5841924520.0610.0999.498.5
4.03-4.663.80.0966.3828721870.0550.09611.798.7
4.66-5.74.30.0986.3808518840.0520.09812.298.5
5.7-8.064.60.0986.3657714300.0490.09811.798.4
8.06-53.7150.0866.342258520.0420.08614.299.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.15data scaling
BUSTER-TNTBUSTER 2.11.4refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→28.68 Å / Cor.coef. Fo:Fc: 0.9272 / Cor.coef. Fo:Fc free: 0.8975 / SU R Cruickshank DPI: 0.443 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.422 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1212 5.15 %RANDOM
Rwork0.1807 ---
obs0.183 23536 94.39 %-
Displacement parametersBiso max: 117.87 Å2 / Biso mean: 37.87 Å2 / Biso min: 6.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.0707 Å20 Å20.4628 Å2
2--1.4547 Å20 Å2
3----1.3839 Å2
Refine analyzeLuzzati coordinate error obs: 0.305 Å
Refinement stepCycle: final / Resolution: 2.55→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4428 0 68 103 4599
Biso mean--35.82 33.08 -
Num. residues----560
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1590SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes708HARMONIC5
X-RAY DIFFRACTIONt_it4602HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion574SEMIHARMONIC5
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_contact5000SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4602HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6214HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion19.06
LS refinement shellResolution: 2.55→2.66 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2841 143 5.4 %
Rwork0.201 2505 -
all0.2055 2648 -
obs--94.39 %
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)
15.6211-0.3461-2.30881.22130.41733.6713-0.0526-0.53-0.47490.2192-0.0340.23730.422-0.47520.0865-0.2395-0.08710.00870.24870.1263-0.2542-3.52465.643634.7504
22.1802-0.030.56320.17930.04652.1276-0.0301-0.179-0.046-0.0265-0.0135-0.00620.04160.03660.0436-0.11240.00730.0180.0090.0003-0.07567.22613.978912.2437
30.9111-0.73270.63250.193-1.66620.9375-0.0057-0.0281-0.04670.05690.00750.00970.01040.0478-0.0018-0.0613-0.0318-0.01730.0680.1491-0.06992.309651.537639.0626
44.70070.83841.70321.161-0.20984.1342-0.12550.55890.5069-0.2110.07830.1723-0.2943-0.51080.0471-0.23110.031-0.01430.22940.1405-0.1928-6.752216.866769.0508
51.66390.1333-0.19570.9262-0.05752.0364-0.03570.2320.09050.06570.0285-0.02860.00720.0290.0073-0.0843-0.0198-0.0259-0.01750.0033-0.07644.028.891.7434
61.25171.5424-0.38050.2431-1.17661.1831-0.00570.03160.0271-0.02950.0134-0.0223-0.02610.0333-0.0077-0.03670.0377-0.01740.01470.1388-0.0219-0.8682-28.960664.9272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|62 - A|151 }A62 - 151
2X-RAY DIFFRACTION2{ A|152 - A|347 }A152 - 347
3X-RAY DIFFRACTION3{ A|354 - A|359 }A354 - 359
4X-RAY DIFFRACTION4{ B|62 - B|151 }B62 - 151
5X-RAY DIFFRACTION5{ B|152 - B|346 }B152 - 346
6X-RAY DIFFRACTION6{ B|354 - B|359 }B354 - 359

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