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- PDB-4jg7: Structure of RSK2 CTD bound to 3-(3-(1H-pyrrolo[2,3-b]pyridine-3-... -

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Basic information

Entry
Database: PDB / ID: 4jg7
TitleStructure of RSK2 CTD bound to 3-(3-(1H-pyrrolo[2,3-b]pyridine-3-carbonyl)phenyl)-2-cyanoacrylamide
ComponentsRibosomal protein S6 kinase alpha-3Ribosome
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein Kinase / Phosphorylation / Covalent Inhibitor / 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-1LC / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.0002 Å
AuthorsMiller, R.M. / Paavilainen, V.O. / Krishnan, S. / Serafimova, I.M. / Taunton, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Electrophilic fragment-based design of reversible covalent kinase inhibitors.
Authors: Miller, R.M. / Paavilainen, V.O. / Krishnan, S. / Serafimova, I.M. / Taunton, J.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.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_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)40,4093
Polymers40,0681
Non-polymers3412
Water39622
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.660, 47.660, 292.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is the same as asym.

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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: 40067.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA3, ISPK1, MAPKAPK1B, RSK2 / Production host: Escherichia coli (E. coli)
References: UniProt: P51812, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-1LC / (2R)-2-cyano-3-[3-(1H-pyrrolo[2,3-b]pyridin-3-ylcarbonyl)phenyl]propanamide


Mass: 318.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14N4O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, 50 mM Ammonium Sulfate, 7.5% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 4, 2009
RadiationMonochromator: Flat Graphite Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→47.6 Å / Num. all: 7446 / Num. obs: 7417 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 3→3.18 Å / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QR8

2qr8


Resolution: 3.0002→47.038 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.91 / σ(F): 0 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2979 742 10 %
Rwork0.2586 --
obs0.2625 7417 99.1 %
all-7484 -
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.943 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7428 Å20 Å20 Å2
2--1.7428 Å20 Å2
3----3.4856 Å2
Refinement stepCycle: LAST / Resolution: 3.0002→47.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 25 22 2378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072421
X-RAY DIFFRACTIONf_angle_d0.4373307
X-RAY DIFFRACTIONf_dihedral_angle_d12.636847
X-RAY DIFFRACTIONf_chiral_restr0.029377
X-RAY DIFFRACTIONf_plane_restr0.002425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.23180.35941440.32561297X-RAY DIFFRACTION100
3.2318-3.55690.33211440.28541292X-RAY DIFFRACTION100
3.5569-4.07130.27621400.25921265X-RAY DIFFRACTION97
4.0713-5.12840.24871510.21281351X-RAY DIFFRACTION100
5.1284-47.04380.30781630.25261470X-RAY DIFFRACTION99

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