[English] 日本語
Yorodumi
- PDB-8r4q: Salt inducible kinase 3 in complex with inhibitor -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more