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- PDB-9iwz: Crystal structure of the mouse RIP3 kinase domain in complexed wi... -

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Basic information

Entry
Database: PDB / ID: 9iwz
TitleCrystal structure of the mouse RIP3 kinase domain in complexed with GSK'843
ComponentsReceptor-interacting serine/threonine-protein kinase 3
KeywordsTRANSFERASE / Mouse RIP3 kinase domain / inhibitor / complex
Function / homology
Function and homology information


RIPK1-mediated regulated necrosis / regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRIF-mediated programmed cell death / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of activated T cell proliferation / Regulation of necroptotic cell death / IKK complex recruitment mediated by RIP1 / regulation of adaptive immune response ...RIPK1-mediated regulated necrosis / regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRIF-mediated programmed cell death / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of activated T cell proliferation / Regulation of necroptotic cell death / IKK complex recruitment mediated by RIP1 / regulation of adaptive immune response / regulation of type II interferon production / activation of protein kinase activity / programmed necrotic cell death / TRP channels / necroptotic signaling pathway / positive regulation of necroptotic process / non-canonical NF-kappaB signal transduction / regulation of reactive oxygen species metabolic process / necroptotic process / T cell homeostasis / lymph node development / positive regulation of intrinsic apoptotic signaling pathway / spleen development / reactive oxygen species metabolic process / thymus development / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / T cell differentiation in thymus / regulation of apoptotic process / defense response to virus / amyloid fibril formation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein-containing complex binding / protein-containing complex / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RHIM domain / RIP homotypic interaction motif / : / 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. ...RHIM domain / RIP homotypic interaction motif / : / 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-ZOV / Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsXie, H. / Su, H.X. / Li, M.J. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structure-based design of potent and selective inhibitors targeting RIPK3 for eliminating on-target toxicity in vitro.
Authors: Su, H. / Chen, G. / Xie, H. / Li, W. / Xiong, M. / He, J. / Hu, H. / Zhao, W. / Shao, Q. / Li, M. / Zhao, Q. / Xu, Y.
History
DepositionJul 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 3
B: Receptor-interacting serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1824
Polymers72,4272
Non-polymers7552
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.790, 49.101, 103.434
Angle α, β, γ (deg.)90.00, 131.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Receptor-interacting serine/threonine-protein kinase 3 / RIP-like protein kinase 3 / Receptor-interacting protein 3 / RIP-3 / mRIP3


Mass: 36213.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ripk3, Rip3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9QZL0, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ZOV / 3-(1,3-benzothiazol-5-yl)-7-(1,3-dimethyl-1H-pyrazol-5-yl)thieno[3,2-c]pyridin-4-amine / GSK'843


Mass: 377.486 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C19H15N5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10-20% PEG3350, 50 mM magnesium formate,pH 5.0-7.5 / PH range: 5.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.82→77.62 Å / Num. obs: 48010 / % possible obs: 94.1 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.028 / Rrim(I) all: 0.059 / Χ2: 0.54 / Net I/σ(I): 10.9 / Num. measured all: 205965
Reflection shellResolution: 1.82→1.92 Å / % possible obs: 93.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.565 / Num. measured all: 30311 / Num. unique obs: 6928 / CC1/2: 0.873 / Rpim(I) all: 0.301 / Rrim(I) all: 0.642 / Χ2: 0.54 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M66

4m66


Resolution: 1.82→35.68 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 2313 4.82 %
Rwork0.1759 --
obs0.1776 47985 94.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4245 0 52 277 4574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114403
X-RAY DIFFRACTIONf_angle_d1.2556009
X-RAY DIFFRACTIONf_dihedral_angle_d9.921630
X-RAY DIFFRACTIONf_chiral_restr0.074687
X-RAY DIFFRACTIONf_plane_restr0.01767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.2521460.21482808X-RAY DIFFRACTION100
1.86-1.90.25311430.2112817X-RAY DIFFRACTION100
1.9-1.940.2563870.20951947X-RAY DIFFRACTION68
1.94-1.990.27621050.19062022X-RAY DIFFRACTION72
1.99-2.040.26671320.18922853X-RAY DIFFRACTION100
2.04-2.10.23981030.18632114X-RAY DIFFRACTION75
2.1-2.170.25621490.19112827X-RAY DIFFRACTION100
2.17-2.250.26071560.18352851X-RAY DIFFRACTION100
2.25-2.340.21961430.17952850X-RAY DIFFRACTION100
2.34-2.440.24841570.18352825X-RAY DIFFRACTION100
2.44-2.570.21821510.18912839X-RAY DIFFRACTION100
2.57-2.730.2131290.18562868X-RAY DIFFRACTION100
2.73-2.950.2661200.18482869X-RAY DIFFRACTION100
2.95-3.240.20491530.17732860X-RAY DIFFRACTION100
3.24-3.710.18071380.16842659X-RAY DIFFRACTION92
3.71-4.670.16461440.14782715X-RAY DIFFRACTION94
4.67-35.680.19821570.17142948X-RAY DIFFRACTION99

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