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- PDB-4jg6: RSK2 CTD bound to 2-cyano-3-(1H-indazol-5-yl)acrylamide -

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Basic information

Entry
Database: PDB / ID: 4jg6
TitleRSK2 CTD bound to 2-cyano-3-(1H-indazol-5-yl)acrylamide
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
(2S)-2-cyano-3-(1H-indazol-5-yl)propanamide / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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

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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)40,3053
Polymers40,0681
Non-polymers2372
Water75742
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.280, 47.280, 291.970
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 / 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-1LB / (2S)-2-cyano-3-(1H-indazol-5-yl)propanamide


Mass: 214.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N4O
#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.: 42 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
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: Aug 18, 2009
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→48.66 Å / Num. obs: 11112 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.6→2.76 Å / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.672 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.86 / σ(F): 1.35 / Phase error: 31.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2986 537 4.83 %
Rwork0.2521 --
obs0.2543 11112 99.97 %
all-11115 -
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.689 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3931 Å20 Å2-0 Å2
2--2.3931 Å2-0 Å2
3----4.7862 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 17 42 2423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132439
X-RAY DIFFRACTIONf_angle_d0.663327
X-RAY DIFFRACTIONf_dihedral_angle_d10.058879
X-RAY DIFFRACTIONf_chiral_restr0.043370
X-RAY DIFFRACTIONf_plane_restr0.003424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.86170.44171370.36682535X-RAY DIFFRACTION100
2.8617-3.27570.35251230.30152579X-RAY DIFFRACTION100
3.2757-4.12660.3111440.24462614X-RAY DIFFRACTION100
4.1266-46.67950.24421330.21772847X-RAY DIFFRACTION100
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)
14.97690.62940.06916.0684-0.90457.8275-0.00850.0466-0.63080.05670.41370.5115-0.1955-1.5951-0.3290.3055-0.1590.10210.55270.03430.36979.2391-34.786812.5373
21.76641.7361-0.44713.18220.94683.84310.10690.1967-0.0374-0.4158-0.05320.0428-0.466-0.4064-0.01210.42880.23850.02850.3235-0.00810.344622.2105-21.844316.4952
33.9169-0.8006-0.74533.18830.15422.5296-0.0147-0.24860.48550.13390.0664-0.1201-0.81820.2018-0.12150.7264-0.0810.11010.1936-0.02530.416727.0133-10.474629.3358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 406:470)
2X-RAY DIFFRACTION2chain 'A' and (resseq 471:613)
3X-RAY DIFFRACTION3chain 'A' and (resseq 614:712)

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