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- PDB-4m8t: RSK2 T493M C-Terminal Kinase Domain in complex with 3-(3-(1H-pyra... -

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Basic information

Entry
Database: PDB / ID: 4m8t
TitleRSK2 T493M C-Terminal Kinase Domain in complex with 3-(3-(1H-pyrazol-4-yl)phenyl)-2-cyanoacrylamide
ComponentsRibosomal protein S6 kinase alpha-3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein Kinase / Phosphorylation / Covalent Inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


RSK activation / CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Gastrin-CREB signalling pathway via PKC and MAPK / Senescence-Associated Secretory Phenotype (SASP) / ribosomal protein S6 kinase activity / ERK/MAPK targets / toll-like receptor signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to lipopolysaccharide ...RSK activation / CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Gastrin-CREB signalling pathway via PKC and MAPK / Senescence-Associated Secretory Phenotype (SASP) / ribosomal protein S6 kinase activity / ERK/MAPK targets / toll-like receptor signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to lipopolysaccharide / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / protein kinase binding / magnesium ion binding / 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-RMM / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMiller, R.M. / Taunton, J.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Covalent docking of large libraries for the discovery of chemical probes.
Authors: London, N. / Miller, R.M. / Krishnan, S. / Uchida, K. / Irwin, J.J. / Eidam, O. / Gibold, L. / Cimermancic, P. / Bonnet, R. / Shoichet, B.K. / Taunton, J.
History
DepositionAug 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,3593
Polymers40,0981
Non-polymers2612
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.990, 46.990, 291.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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


Mass: 40097.645 Da / Num. of mol.: 1
Fragment: RSK2 C-terminal Kinase Domain, UNP residues 400-720
Mutation: T493M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rps6ka3, Mapkapk1b, Rps6ka-rs1, Rsk2 / Production host: Escherichia coli (E. coli)
References: UniProt: P18654, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-RMM / (2E)-2-cyano-3-[3-(1H-pyrazol-4-yl)phenyl]prop-2-enamide


Mass: 238.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10N4O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has protein modificationY

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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 Å3/Da / Density % sol: 38.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, 50 mM Ammonium Sulfate, 7.5% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999974 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2013
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999974 Å / Relative weight: 1
ReflectionResolution: 2.6→46.4 Å / Num. obs: 7265 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.6→2.9 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→46.389 Å / SU ML: 0.43 / σ(F): 0 / Phase error: 29.6 / Stereochemistry target values: ML
Details: I/SIGMAS WERE EXTREMELY LOW FOR THE HIGH RESOLUTION REFLECTIONS, AS WAS THE COMPLETENESS. THE AUTHORS TRUNCATED THE DATA USED IN REFINEMENT TO ONLY INCLUDE DATA WITH HIGH ENOUGH INTENSITY AND COMPLETENESS.
RfactorNum. reflection% reflectionSelection details
Rfree0.3107 348 4.85 %Random
Rwork0.252 ---
all0.2548 7265 --
obs0.2548 7176 98.77 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.921 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8595 Å20 Å2-0 Å2
2--5.8595 Å2-0 Å2
3----11.719 Å2
Refinement stepCycle: LAST / Resolution: 3→46.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 19 0 2389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012449
X-RAY DIFFRACTIONf_angle_d0.9593325
X-RAY DIFFRACTIONf_dihedral_angle_d15.197883
X-RAY DIFFRACTIONf_chiral_restr0.057368
X-RAY DIFFRACTIONf_plane_restr0.005427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.77980.37411810.29993293X-RAY DIFFRACTION99
3.7798-46.3890.27521670.22833535X-RAY DIFFRACTION98

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