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- PDB-8r4o: Salt inducible kinase 3 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 8r4o
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 / protein phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / 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 / protein phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Salt-Inducible kinase, catalytic domain / Protein kinase SIK3 UBA 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. ...Salt-Inducible kinase, catalytic domain / Protein kinase SIK3 UBA 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
: / Serine/threonine-protein kinase SIK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.725 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 1.3Nov 6, 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

Downloads & links

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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)400,96424
Polymers397,63712
Non-polymers3,32712
Water2,162120
1
A: Serine/threonine-protein kinase SIK3
B: scFvH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8274
Polymers66,2732
Non-polymers5542
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)66,9235
Polymers66,2732
Non-polymers6513
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)66,7313
Polymers66,2732
Non-polymers4581
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)66,8274
Polymers66,2732
Non-polymers5542
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)66,8274
Polymers66,2732
Non-polymers5542
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)66,8274
Polymers66,2732
Non-polymers5542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.777, 217.658, 223.116
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: 28384.033 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-XVI / 2-[bis(fluoranyl)methoxy]-4-[6-(2-cyanopropan-2-yl)pyrazolo[1,5-a]pyridin-3-yl]-~{N}-[(1~{R},2~{S})-2-fluoranylcyclopropyl]-6-methoxy-benzamide


Mass: 458.433 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H21F3N4O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.72→155.8 Å / Num. obs: 80912 / % possible obs: 73.7 % / Redundancy: 5.5 % / CC1/2: 0.998 / Net I/σ(I): 12.6
Reflection shellResolution: 2.72→2.97 Å / Num. unique obs: 4047 / CC1/2: 0.531

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.725→155.8 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.407
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 4057 -RANDOM
Rwork0.2142 ---
obs0.2156 80912 73.7 %-
Displacement parametersBiso mean: 75.53 Å2
Baniso -1Baniso -2Baniso -3
1--2.3731 Å20 Å20 Å2
2--2.0109 Å20 Å2
3---0.3622 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.725→155.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25904 0 228 120 26252
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00726716HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.936266HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8960SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4527HARMONIC5
X-RAY DIFFRACTIONt_it26716HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3460SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact19032SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion19.17
LS refinement shellResolution: 2.73→2.89 Å
RfactorNum. reflection% reflection
Rfree0.4311 88 -
Rwork0.3413 --
obs0.3459 1619 9.46 %
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)
11.7223-0.4080.22863.18130.84273.3050.0747-0.3414-0.2034-0.34140.0071-0.2066-0.2034-0.2066-0.0818-0.01280.1166-0.10440.09960.0339-0.2353-15.64712.3404-100.775
22.8658-1.128-1.50181.96040.86036.55880.0134-0.0171-0.1982-0.01710.056-0.2969-0.1982-0.2969-0.06930.08110.1653-0.0105-0.12180.0371-0.1228-20.787328.1364-64.7261
32.4013-1.10720.22712.7286-0.95482.92660.053-0.1350.7901-0.135-0.0186-0.22290.7901-0.2229-0.03450.0004-0.3719-0.128-0.2830.09930.17156.524461.76-72.5082
43.3205-2.32150.46145.0418-0.22321.69880.0337-0.25370.0455-0.25370.0514-0.28010.0455-0.2801-0.085-0.0371-0.2778-0.0642-0.02960.0517-0.1485-4.179397.4415-86.1022
52.6387-0.09540.04773.025-1.09992.3069-0.0240.358-0.97740.3580.0559-0.1253-0.9774-0.1253-0.03190.35460.16180.177-0.3154-0.0055-0.0093-20.127645.2925-23.3899
62.04281.58130.24573.78671.29341.2663-0.0841-0.0725-0.1696-0.07250.2276-0.1404-0.1696-0.1404-0.1435-0.09960.2090.1504-0.05930.11590.0299-32.26768.0481-30.0677
71.9997-0.07710.10361.82890.5313.72850.1005-0.3130.21-0.3130.0570.26540.210.2654-0.1575-0.1344-0.1066-0.0094-0.1692-0.01890.0949-43.506373.1829-76.3031
82.59410.27420.3163.96962.08283.13950.1532-0.0315-0.2292-0.0315-0.06180.1482-0.22920.1482-0.0914-0.1607-0.1423-0.12430.19220.0498-0.1336-52.467296.7324-45.0424
92.3388-0.0731-0.30552.0064-0.4194.9280.0610.3876-0.51150.38760.0820.6578-0.51150.6578-0.14310.1518-0.0699-0.0352-0.0848-0.1283-0.21879.992329.9636-10.9543
103.1463-0.9724-0.86782.36491.87464.70880.0613-0.0971-0.374-0.09710.02640.7802-0.3740.7802-0.0878-0.1102-0.03350.020.1826-0.0338-0.139916.965820.52-48.9965
112.549-0.636-0.12363.6699-0.96533.47780.157-0.273-0.5783-0.2730.03571.4468-0.57831.4468-0.1927-0.3269-0.02740.11730.6395-0.1832-0.412819.210812.0705-92.7485
121.6561-0.1946-0.31162.8934-2.93236.2040.3224-0.15640.3389-0.1564-0.20941.02540.33891.0254-0.1131-0.27690.2681-0.06950.3625-0.1928-0.12499.9125-16.3584-66.3898
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 - 264
7X-RAY DIFFRACTION5{ E|* }E62 - 384
8X-RAY DIFFRACTION5{ E|* }E459
9X-RAY DIFFRACTION6{ F|* }F1 - 265
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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