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- PDB-8r4q: Salt inducible kinase 3 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 8r4q
TitleSalt inducible kinase 3 in complex with inhibitor
Components
  • Serine/threonine-protein kinase SIK3
  • scFvH1
KeywordsLIGASE / Kinase Inhibitor complex AMPK-like salt-induced kinase
Function / homology
Function and homology information


positive regulation of TORC2 signaling / tau-protein kinase activity / positive regulation of TORC1 signaling / microtubule cytoskeleton organization / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding ...positive regulation of TORC2 signaling / tau-protein kinase activity / positive regulation of TORC1 signaling / microtubule cytoskeleton organization / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Salt-Inducible kinase, catalytic domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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. ...Salt-Inducible kinase, catalytic domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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
Similarity search - Domain/homology
Chem-DB8 / Serine/threonine-protein kinase SIK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.838 Å
AuthorsKack, H. / Oster, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The structures of salt-inducible kinase 3 in complex with inhibitors reveal determinants for binding and selectivity.
Authors: Oster, L. / Castaldo, M. / de Vries, E. / Edfeldt, F. / Pemberton, N. / Gordon, E. / Cederblad, L. / Kack, H.
History
DepositionNov 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 8, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase SIK3
B: scFvH1
C: Serine/threonine-protein kinase SIK3
D: scFvH1
E: Serine/threonine-protein kinase SIK3
F: scFvH1
G: Serine/threonine-protein kinase SIK3
H: scFvH1
I: Serine/threonine-protein kinase SIK3
J: scFvH1
K: Serine/threonine-protein kinase SIK3
L: scFvH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,84727
Polymers391,79912
Non-polymers4,04715
Water1,26170
1
A: Serine/threonine-protein kinase SIK3
B: scFvH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9264
Polymers65,3002
Non-polymers6272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Serine/threonine-protein kinase SIK3
D: scFvH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0225
Polymers65,3002
Non-polymers7233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Serine/threonine-protein kinase SIK3
F: scFvH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0225
Polymers65,3002
Non-polymers7233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Serine/threonine-protein kinase SIK3
H: scFvH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9264
Polymers65,3002
Non-polymers6272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Serine/threonine-protein kinase SIK3
J: scFvH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9264
Polymers65,3002
Non-polymers6272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Serine/threonine-protein kinase SIK3
L: scFvH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0225
Polymers65,3002
Non-polymers7233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.116, 213.702, 223.656
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Serine/threonine-protein kinase SIK3


Mass: 37888.852 Da / Num. of mol.: 6 / Mutation: C121S, C181S, C333S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIK3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y2K2
#2: Protein
scFvH1


Mass: 27411.029 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical
ChemComp-DB8 / 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile / Bosutinib


Mass: 530.446 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H29Cl2N5O3 / Comment: inhibitor, medication*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 8000, 20% 1,5-Pentanediol, 0.03 M Lithium sulfate, 0.03 M Sodium sulfate, 0.03 M Potassium sulfate and 0.1 M Buffer system 4 pH 6.5 (Mopso, Bis-Tris)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.838→111.8 Å / Num. obs: 79167 / % possible obs: 80.5 % / Redundancy: 6.9 % / CC1/2: 0.994 / Net I/σ(I): 9.7
Reflection shellResolution: 2.84→3.06 Å / Redundancy: 7 % / Num. unique obs: 3959 / CC1/2: 0.615 / % possible all: 20.4

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.838→41.26 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.414
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 4205 -RANDOM
Rwork0.2123 ---
obs0.214 79135 81.4 %-
Displacement parametersBiso mean: 86.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.7542 Å20 Å20 Å2
2--3.1843 Å20 Å2
3----0.4301 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.838→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26031 0 261 70 26362
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00726877HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.936440HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9069SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4556HARMONIC5
X-RAY DIFFRACTIONt_it26877HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3447SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact19466SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion19.12
LS refinement shellResolution: 2.84→2.99 Å
RfactorNum. reflection% reflection
Rfree0.3855 92 -
Rwork0.3252 --
obs0.3287 1583 11.65 %
Refinement TLS params.

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)
11.81640.00770.75563.56570.78932.99660.1164-0.5202-0.1125-0.52020.1322-0.2587-0.1125-0.2587-0.24860.3373-0.1602-0.13380.22170.1214-0.0326-16.415812.5391-100.909
22.4076-0.6833-1.87331.99240.96636.5544-0.0501-0.0386-0.2667-0.03860.0822-0.1427-0.2667-0.1427-0.03210.2186-0.0642-0-0.11840.12150.0012-20.617828.4135-64.7826
32.0787-0.30460.55591.8312-0.67372.0340.03490.28840.75760.2884-0.0826-0.38850.7576-0.38850.04760.5784-0.39840.2130.109-0.10120.39918.692259.7876-72.7581
43.1201-1.74560.36124.3698-0.05382.2343-0.04850.0760.15210.076-0.0283-0.54720.1521-0.54720.07680.0144-0.19940.11670.2303-0.13650.0393-3.004194.4435-85.7366
52.67140.5936-0.44993.8288-0.78122.81950.15960.3549-1.08810.3549-0.0190.027-1.08810.027-0.14060.6415-0.02720.227-0.0573-0.06490.1977-19.170945.2657-23.2118
63.37780.72320.54334.84850.91512.6913-0.1499-0.0444-0.2336-0.04440.1905-0.0795-0.2336-0.0795-0.0406-0.0550.10870.2368-0.04170.10840.1969-31.83089.3927-29.3918
72.383-0.4137-0.25322.47391.4474.40260.0815-0.65040.0806-0.65040.14470.50430.08060.5043-0.22620.2402-0.05050.27060.0223-0.07920.3565-43.286372.097-76.3767
82.0147-1.0678-0.70086.54174.23035.1682-0.0375-0.2391-0.4774-0.23910.24060.24-0.47740.24-0.2031-0.09260.0110.02980.1205-0.07480.1763-52.246895.8397-45.3261
92.23660.606-0.5412.265-0.87873.8298-0.0050.4814-0.83240.48140.07730.9157-0.83240.9157-0.07230.2152-0.39710.05560.4753-0.1287-0.057610.781829.7898-11.6922
102.9035-1.5479-2.05283.7663.5936.8515-0.0252-0.225-0.4921-0.2250.15811.3737-0.49211.3737-0.1329-0.0382-0.40730.04930.46260.0314-0.152217.072219.3968-49.4595
111.9731-0.5272-0.36953.7103-0.15162.3762-0.0377-0.0213-0.8147-0.02130.00470.6593-0.81470.65930.0330.2377-0.30330.06610.58960.00740.016618.668910.0018-93.1575
121.1812-0.4813-0.22232.6951-2.48546.103-0.11250.11190.03580.11190.03650.85170.03580.85170.076-0.17650.13520.15760.5630.13340.01418.2687-17.6103-67.0548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A62 - 384
2X-RAY DIFFRACTION1{ A|* }A459
3X-RAY DIFFRACTION2{ B|* }B1 - 264
4X-RAY DIFFRACTION3{ C|* }C62 - 384
5X-RAY DIFFRACTION3{ C|* }C459
6X-RAY DIFFRACTION4{ D|* }D1 - 263
7X-RAY DIFFRACTION5{ E|* }E62 - 384
8X-RAY DIFFRACTION5{ E|* }E459
9X-RAY DIFFRACTION6{ F|* }F1 - 262
10X-RAY DIFFRACTION7{ G|* }G62 - 384
11X-RAY DIFFRACTION7{ G|* }G459
12X-RAY DIFFRACTION8{ H|* }H1 - 264
13X-RAY DIFFRACTION9{ I|* }I62 - 384
14X-RAY DIFFRACTION9{ I|* }I459
15X-RAY DIFFRACTION10{ J|* }J1 - 264
16X-RAY DIFFRACTION11{ K|* }K62 - 384
17X-RAY DIFFRACTION11{ K|* }K459
18X-RAY DIFFRACTION12{ L|* }L1 - 264

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