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- PDB-3wf5: Crystal structure of S6K1 kinase domain in complex with a pyrazol... -

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Basic information

Entry
Database: PDB / ID: 3wf5
TitleCrystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative 4-[4-(1H-benzimidazol-2-yl)piperidin-1-yl]-1H-pyrazolo[3,4-d]pyrimidine
ComponentsRibosomal protein S6 kinase beta-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SERINE/THREONINE PROTEIN KINASE DOMAIN / TRANSFERASE / PHOSPHORYLATION / ATP-BINDING / ZINC-BINDING / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / positive regulation of skeletal muscle tissue growth / regulation of D-glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / response to glucagon / positive regulation of smooth muscle cell migration ...long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / positive regulation of skeletal muscle tissue growth / regulation of D-glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / response to glucagon / positive regulation of smooth muscle cell migration / response to testosterone / mTORC1-mediated signalling / germ cell development / phosphatidylinositol-mediated signaling / skeletal muscle contraction / behavioral fear response / TOR signaling / response to tumor necrosis factor / positive regulation of translational initiation / long-term memory / response to glucose / response to mechanical stimulus / negative regulation of insulin receptor signaling pathway / protein serine/threonine/tyrosine kinase activity / positive regulation of TORC1 signaling / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / response to nutrient levels / protein phosphatase 2A binding / positive regulation of translation / negative regulation of extrinsic apoptotic signaling pathway / PDZ domain binding / positive regulation of smooth muscle cell proliferation / peptide binding / modulation of chemical synaptic transmission / cellular response to growth factor stimulus / cellular response to type II interferon / response to toxic substance / cellular response to insulin stimulus / G1/S transition of mitotic cell cycle / cell migration / peptidyl-serine phosphorylation / response to ethanol / mitochondrial outer membrane / postsynapse / response to lipopolysaccharide / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / cell surface / signal transduction / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S6 kinase / 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 ...Ribosomal protein S6 kinase / 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-FZ8 / Ribosomal protein S6 kinase beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsNiwa, H. / Shirouzu, M. / Yokoyama, S.
CitationJournal: J.Struct.Funct.Genom. / Year: 2014
Title: Crystal structures of the S6K1 kinase domain in complexes with inhibitors
Authors: Niwa, H. / Mikuni, J. / Sasaki, S. / Tomabechi, Y. / Honda, K. / Ikeda, M. / Ohsawa, N. / Wakiyama, M. / Handa, N. / Shirouzu, M. / Honma, T. / Tanaka, A. / Yokoyama, S.
History
DepositionJul 17, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5643
Polymers37,1791
Non-polymers3852
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.217, 69.217, 143.181
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 beta-1 / S6K-beta-1 / S6K1 / 70 kDa ribosomal protein S6 kinase 1 / Ribosomal protein S6 kinase I / ...S6K-beta-1 / S6K1 / 70 kDa ribosomal protein S6 kinase 1 / Ribosomal protein S6 kinase I / Serine/threonine-protein kinase 14A / p70 ribosomal S6 kinase alpha


Mass: 37178.816 Da / Num. of mol.: 1 / Fragment: UNP residues 78-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P23443, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FZ8 / 4-[4-(1H-benzimidazol-2-yl)piperidin-1-yl]-1H-pyrazolo[3,4-d]pyrimidine


Mass: 319.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 2.9-3.3M sodium formate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 25, 2011
RadiationMonochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. all: 20923 / Num. obs: 20923 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Rsym value: 0.08 / Net I/σ(I): 30
Reflection shellResolution: 2.099→2.14 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 994 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.099→40.404 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1946 5.05 %RANDOM
Rwork0.1748 20901 --
obs0.1775 20901 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.67 Å2 / Biso mean: 49.7192 Å2 / Biso min: 21.33 Å2
Refinement stepCycle: LAST / Resolution: 2.099→40.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 25 110 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082300
X-RAY DIFFRACTIONf_angle_d1.0543101
X-RAY DIFFRACTIONf_chiral_restr0.045330
X-RAY DIFFRACTIONf_plane_restr0.005392
X-RAY DIFFRACTIONf_dihedral_angle_d16.465876
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0994-2.15190.31681430.28412582272599
2.1519-2.21010.26781250.24922615274099
2.2101-2.27510.25541440.22592598274299
2.2751-2.34860.27141510.21472570272199
2.3486-2.43250.23731580.19132590274899
2.4325-2.52990.2091430.18672612275599
2.5299-2.6450.26381570.19422632278999
2.645-2.78440.25721330.19062602273599
2.7844-2.95880.2481540.18672610276499
2.9588-3.18720.2771300.177426352765100
3.1872-3.50780.22241340.168626342768100
3.5078-4.01490.20821210.15526332754100
4.0149-5.05690.2161430.137126362779100
5.0569-40.41140.20431100.173526652775100
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)
13.67150.17751.39777.94970.76268.01850.0695-0.53210.1810.37850.15-0.48150.28020.7662-0.18570.22010.00590.02790.4478-0.09860.2724-3.04875.4276-16.4602
25.1181-2.2059-2.68033.40041.44963.4171-0.2982-0.2661-0.49460.17610.0640.14860.32620.30490.22880.2811-0.01370.03870.3097-0.00790.2604-18.37487.4868-7.3579
33.4989-2.132-1.85743.1851.99655.1331-0.0978-0.1353-0.21750.14190.04780.1349-0.01720.02810.03170.2317-0.02820.06460.32070.01980.2606-28.079816.7783-0.6877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 85:126 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 127:234 )
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 235:374 )

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