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- PDB-4d9t: Rsk2 C-terminal Kinase Domain with inhibitor (E)-methyl 3-(4-amin... -

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Basic information

Entry
Database: PDB / ID: 4d9t
TitleRsk2 C-terminal Kinase Domain with inhibitor (E)-methyl 3-(4-amino-7-(3-hydroxypropyl)-5-p-tolyl-7H-pyrrolo[2,3-d]pyrimidin-6-yl)-2-cyanoacrylate
ComponentsRibosomal protein S6 kinase alpha-3Ribosome
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / inhibitor / reversible / thiol / phosphorylation / migration / 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-0JG / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSerafimova, I.M. / Pufall, M.A. / Krishnan, S. / Duda, K. / Cohen, M.S. / Maglathlin, R.L. / McFarland, J.M. / Miller, R.M. / Frodin, M. / Taunton, J.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: Reversible targeting of noncatalytic cysteines with chemically tuned electrophiles.
Authors: Serafimova, I.M. / Pufall, M.A. / Krishnan, S. / Duda, K. / Cohen, M.S. / Maglathlin, R.L. / McFarland, J.M. / Miller, R.M. / Frodin, M. / Taunton, J.
History
DepositionJan 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: 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)38,8933
Polymers38,4791
Non-polymers4142
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ribosomal protein S6 kinase alpha-3
hetero molecules

A: Ribosomal protein S6 kinase alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7876
Polymers76,9582
Non-polymers8294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area1940 Å2
ΔGint-9 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.700, 46.700, 294.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 38478.930 Da / Num. of mol.: 1 / Fragment: C-terminal kinase domain, UNP residues 399-740
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISPK1, MAPKAPK1B, RPS6KA3, RSK2 / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P51812, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-0JG / methyl (2S)-3-{4-amino-7-[(1E)-3-hydroxyprop-1-en-1-yl]-5-(4-methylphenyl)-7H-pyrrolo[2,3-d]pyrimidin-6-yl}-2-cyanopropanoate / (E)-methyl 3-(4-amino-7-(3-hydroxypropyl)-5-p-tolyl-7H-pyrrolo[2,3-d]pyrimidin-6-yl)-2-cyanoacrylate


Mass: 391.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N5O3
#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.: 24 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 8.5
Details: 100mM Tris, pH 8.5, 25% PEG 3350, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→36.6 Å / Num. all: 13794 / Num. obs: 13507 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 62.4 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.118 / Net I/σ(I): 18.4
Reflection shellHighest resolution: 2.4 Å / % possible all: 98

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_613refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→36.574 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7921 / SU ML: 0.35 / σ(F): 1.99 / σ(I): 2 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 1350 10 %10% Random
Rwork0.2157 ---
all0.221 13794 --
obs0.221 13506 97.95 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.184 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 257.05 Å2 / Biso mean: 68.6751 Å2 / Biso min: 29.67 Å2
Baniso -1Baniso -2Baniso -3
1-6.3476 Å20 Å2-0 Å2
2--6.3476 Å20 Å2
3----12.6953 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 30 24 2423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012460
X-RAY DIFFRACTIONf_angle_d1.2633334
X-RAY DIFFRACTIONf_chiral_restr0.086367
X-RAY DIFFRACTIONf_plane_restr0.005426
X-RAY DIFFRACTIONf_dihedral_angle_d16.794907
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.48580.38691310.33091182131397
2.4858-2.58530.36641300.29611170130098
2.5853-2.70290.34871280.27361153128197
2.7029-2.84540.33871310.251186131797
2.8454-3.02360.27911320.24221186131898
3.0236-3.25690.27861330.23221201133498
3.2569-3.58440.28991370.20681225136298
3.5844-4.10250.21251340.19381216135098
4.1025-5.16640.18851400.17281258139898
5.1664-36.57850.30051540.21681379153399
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)
11.24490.3446-0.95781.60960.51921.8805-0.1905-0.4098-0.10.34060.13120.06410.49820.3212-0.060.51470.2261-0.01580.48610.0170.3215-27.486317.0594-15.2539
21.108-0.8653-0.25532.56610.78522.3975-0.1146-0.17690.0877-0.30040.4632-0.139-0.39820.6415-0.14520.3025-0.0013-0.01710.6269-0.06530.3601-12.127826.5255-28.5027
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 415:594)A415 - 594
2X-RAY DIFFRACTION2chain 'A' and (resseq 595:713)A595 - 713

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