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- PDB-4nw5: Rsk2 N-terminal kinase in complex with 2-amino-7-substituted benz... -

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Basic information

Entry
Database: PDB / ID: 4nw5
TitleRsk2 N-terminal kinase in complex with 2-amino-7-substituted benzoxazole compound 8
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. / 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-2NR / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsAppleton, B.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: 2-Amino-7-substituted benzoxazole analogs as potent RSK2 inhibitors.
Authors: Costales, A. / Mathur, M. / Ramurthy, S. / Lan, J. / Subramanian, S. / Jain, R. / Atallah, G. / Setti, L. / Lindvall, M. / Appleton, B.A. / Ornelas, E. / Feucht, P. / Warne, B. / Doyle, L. / ...Authors: Costales, A. / Mathur, M. / Ramurthy, S. / Lan, J. / Subramanian, S. / Jain, R. / Atallah, G. / Setti, L. / Lindvall, M. / Appleton, B.A. / Ornelas, E. / Feucht, P. / Warne, B. / Doyle, L. / Basham, S.E. / Aronchik, I. / Jefferson, A.B. / Shafer, C.M.
History
DepositionDec 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 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)37,6292
Polymers37,2051
Non-polymers4241
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.830, 60.540, 112.060
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 / Ribosome / 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-2NR / 7-(2-fluoro-6-methoxyphenyl)-N-(3,4,5-trimethoxyphenyl)-1,3-benzoxazol-2-amine


Mass: 424.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21FN2O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 7-8 mg/mL protein mixed 1:1:0.5 with 12-24% PEG3350 plus 100 mM sodium malonate pH 5-7 and microseeds, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.94→47.04 Å / Num. obs: 26981 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 22.36 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 13
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 6 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2645 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
PROCESSdata reduction
PROCESSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→47.04 Å / Cor.coef. Fo:Fc: 0.9455 / Cor.coef. Fo:Fc free: 0.9249 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 1325 4.95 %RANDOM
Rwork0.173 ---
obs0.1752 26757 99.79 %-
Displacement parametersBiso mean: 25.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.7872 Å20 Å20 Å2
2--3.3506 Å20 Å2
3----2.5634 Å2
Refine analyzeLuzzati coordinate error obs: 0.208 Å
Refinement stepCycle: LAST / Resolution: 1.94→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 31 213 2699
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012573HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.023466HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d927SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes403HARMONIC5
X-RAY DIFFRACTIONt_it2573HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion15.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion314SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3132SEMIHARMONIC4
LS refinement shellResolution: 1.94→2.02 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2453 150 5.05 %
Rwork0.1951 2818 -
all0.1976 2968 -
obs--99.79 %
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)
11.036-2.79081.571700.99083.02930.003-0.03550.03890.46410.014-0.2161-0.1623-0.1075-0.017-0.00260.0099-0.1270.01390.0056-0.044413.3464-15.006-41.5312
21.3809-0.43690.11241.08990.74083.7050.06630.21520.059-0.22080.00820.0424-0.22170.402-0.0745-0.0433-0.03090.00660.0766-0.0295-0.1498-8.4796-2.4359-29.3209
31.18590.2633-0.05390.92970.26820.7356-0.07990.0123-0.04380.0080.0704-0.00730.0466-0.00090.0095-0.05610.0032-0.00490.0244-0.0013-0.0997-12.2541.7858-4.5692
40.1309-2.1158-0.40291.75670.37911.01390.00990.0126-0.047-0.054-0.0244-0.02960.11870.08030.01450.02770.03570.03590.1073-0.0651-0.1376-52.4891-9.5645-30.8231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|51 - A|61 }
2X-RAY DIFFRACTION2{ A|62 - A|151 }
3X-RAY DIFFRACTION3{ A|152 - A|346 }
4X-RAY DIFFRACTION4{ A|354 - A|359 }

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