[English] 日本語
Yorodumi
- PDB-7z4v: Structure of Serine-Threonine kinase STK25 in complex with compound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z4v
TitleStructure of Serine-Threonine kinase STK25 in complex with compound
ComponentsSerine/threonine-protein kinase 25
KeywordsONCOPROTEIN / tumor suppressor / phosphorylation / YAP/TAZ / kinase
Function / homology
Function and homology information


intrinsic apoptotic signaling pathway in response to hydrogen peroxide / Golgi localization / Golgi reassembly / positive regulation of stress-activated MAPK cascade / establishment of Golgi localization / establishment or maintenance of cell polarity / positive regulation of axonogenesis / axonogenesis / cellular response to oxidative stress / response to oxidative stress ...intrinsic apoptotic signaling pathway in response to hydrogen peroxide / Golgi localization / Golgi reassembly / positive regulation of stress-activated MAPK cascade / establishment of Golgi localization / establishment or maintenance of cell polarity / positive regulation of axonogenesis / axonogenesis / cellular response to oxidative stress / response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular exosome / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Serine/threonine kinase 25, catalytic domain / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / 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-IB5 / Serine/threonine-protein kinase 25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.644 Å
AuthorsNawrotek, A. / Vuillard, L. / Miallau, L.
Funding support France, 1items
OrganizationGrant numberCountry
Not funded France
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2022
Title: Targeting non-alcoholic fatty liver disease: Design, X-ray co-crystal structure and synthesis of 'first-in-kind' inhibitors of serine/threonine kinase25.
Authors: Kiyeleko, S. / Hocine, S. / Mautino, G. / Kuenemann, M. / Nawrotek, A. / Miallau, L. / Vuillard, L.M. / Mirguet, O. / Kotschy, A. / Hanessian, S.
History
DepositionMar 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3563
Polymers33,9181
Non-polymers4392
Water2,918162
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint3 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.2, 46.413, 57.954
Angle α, β, γ (deg.)90, 90.56, 90
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Serine/threonine-protein kinase 25 / Ste20-like kinase / Sterile 20/oxidant stress-response kinase 1 / SOK-1 / Ste20/oxidant stress ...Ste20-like kinase / Sterile 20/oxidant stress-response kinase 1 / SOK-1 / Ste20/oxidant stress response kinase 1


Mass: 33917.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphorylated threonine / Source: (gene. exp.) Homo sapiens (human) / Gene: STK25, SOK1, YSK1 / Production host: Escherichia coli (E. coli)
References: UniProt: O00506, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-IB5 / ~{N}-(5-~{tert}-butyl-1~{H}-pyrazol-3-yl)-4-pyrrolidin-1-ylsulfonyl-benzamide


Mass: 376.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 22 % PEG 3350, 0.1 M Bis-tris propane pH 8.5, 0.2 M Potassium citrate, 10 % ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→63.1 Å / Num. obs: 27829 / % possible obs: 92.3 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.065 / Rrim(I) all: 0.121 / Net I/σ(I): 10
Reflection shellResolution: 1.65→1.828 Å / Rmerge(I) obs: 1.123 / Num. unique obs: 1391 / CC1/2: 0.678 / % possible all: 65.7

-
Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KIX

2kix


Resolution: 1.644→63.1 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.174 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.175 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2834 1308 -RANDOM
Rwork0.2451 ---
obs0.247 27829 67.8 %-
Displacement parametersBiso mean: 30.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.4697 Å20 Å2-0.0311 Å2
2---0.2088 Å20 Å2
3----0.2609 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 1.644→63.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 30 162 2535
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082449HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.913317HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d876SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes417HARMONIC5
X-RAY DIFFRACTIONt_it2443HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion316SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2156SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion15.51
LS refinement shellResolution: 1.644→1.76 Å
RfactorNum. reflection% reflection
Rfree0.3337 37 -
Rwork0.2746 --
obs--7.43 %

+
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://pdbjlvh1.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