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- PDB-4nus: Rsk2 N-terminal kinase in complex with LJH685 -

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Basic information

Entry
Database: PDB / ID: 4nus
TitleRsk2 N-terminal kinase in complex with LJH685
ComponentsRibosomal protein S6 kinase alpha-3
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 / ERK/MAPK targets / Recycling pathway of L1 / 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 / ERK/MAPK targets / Recycling pathway of L1 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / : / skeletal system development / central nervous system development / positive regulation of cell differentiation / Senescence-Associated Secretory Phenotype (SASP) / peptidyl-serine phosphorylation / positive regulation of cell growth / chemical synaptic transmission / response to lipopolysaccharide / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / synapse / negative regulation of apoptotic process / nucleolus / 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...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. / 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
Chem-2NK / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsAppleton, B.A.
CitationJournal: 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
DepositionDec 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Ribosomal protein S6 kinase alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5862
Polymers37,2051
Non-polymers3811
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.271, 62.812, 117.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosomal protein S6 kinase alpha-3 / S6K-alpha-3 / 90 kDa ribosomal protein S6 kinase 3 / p90-RSK 3 / p90RSK3 / Insulin-stimulated ...S6K-alpha-3 / 90 kDa ribosomal protein S6 kinase 3 / p90-RSK 3 / p90RSK3 / Insulin-stimulated protein kinase 1 / ISPK-1 / MAP kinase-activated protein kinase 1b / MAPK-activated protein kinase 1b / MAPKAP kinase 1b / MAPKAPK-1b / Ribosomal S6 kinase 2 / RSK-2 / pp90RSK2


Mass: 37204.988 Da / Num. of mol.: 1 / Fragment: N-terminal domain (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-2NK / 2,6-difluoro-4-{4-[4-(4-methylpiperazin-1-yl)phenyl]pyridin-3-yl}phenol


Mass: 381.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21F2N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 12-24% PEG3350, 100 mM sodium malonate pH 5-7, microseeding, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→47.74 Å / Num. obs: 15841 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 55.44 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 13
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 6 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1562 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
PROCESSdata reduction
PROCESSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→47.74 Å / Cor.coef. Fo:Fc: 0.9438 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 764 4.84 %RANDOM
Rwork0.1893 ---
obs0.1911 15789 99.45 %-
Displacement parametersBiso mean: 51.51 Å2
Baniso -1Baniso -2Baniso -3
1--1.7304 Å20 Å20 Å2
2---5.7578 Å20 Å2
3---7.4881 Å2
Refine analyzeLuzzati coordinate error obs: 0.309 Å
Refinement stepCycle: LAST / Resolution: 2.39→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 28 50 2476
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012499HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.073375HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d872SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes386HARMONIC5
X-RAY DIFFRACTIONt_it2499HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion18.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion310SEMIHARMONIC5
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_contact2681SEMIHARMONIC4
LS refinement shellResolution: 2.39→2.56 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2647 139 5.09 %
Rwork0.2091 2593 -
all0.2119 2732 -
obs--99.45 %
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)
10-2.89260.90180.36891.01544.35620.0096-0.03210.04850.1789-0.0355-0.0696-0.06270.03170.0259-0.02950.0390.02660.19820.0067-0.146210.7059-12.1505-44.6432
21.1587-1.3251-0.01690.88610.67455.6172-0.01820.28160.1543-0.3684-0.1132-0.0425-0.5134-0.34830.13130.05590.08780.0109-0.0617-0.0466-0.1888-8.19052.4876-32.1214
32.33120.153-0.56221.4110.33552.0672-0.1017-0.0287-0.18360.04190.0057-0.00670.3321-0.00760.0961-0.06120.0127-0.0023-0.035-0.0068-0.1509-12.19873.5287-6.7829
40.4329-1.5126-1.5520.35370.42441.070.01440.0295-0.0289-0.0091-0.0199-0.0069-0.01660.1160.00550.11560.0550.15190.0046-0.0425-0.1228-52.4756-4.2576-34.3194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|53 - A|61 }
2X-RAY DIFFRACTION2{ A|62 - A|151 }
3X-RAY DIFFRACTION3{ A|152 - A|347 }
4X-RAY DIFFRACTION4{ A|354 - A|359 }

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