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

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Basic information

Entry
Database: PDB / ID: 9iww
TitleCrystal structure of the mouse RIP3 kinase domain in complexed with GSK'872
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 / spleen development / positive regulation of intrinsic apoptotic signaling pathway / 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 / protein kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein-containing complex binding / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
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
: / Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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

Downloads & links

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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)73,1944
Polymers72,4272
Non-polymers7672
Water4,053225
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)149.312, 48.904, 103.382
Angle α, β, γ (deg.)90.00, 131.33, 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-A1D96 / ~{N}-(6-propan-2-ylsulfonylquinolin-4-yl)-1,3-benzothiazol-5-amine / GSK'872


Mass: 383.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C19H17N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 1.96 Å3/Da / Density % sol: 37.14 %
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: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 42598 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Rrim(I) all: 0.09 / Χ2: 0.624 / Net I/σ(I): 4.6 / Num. measured all: 282899
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.93-1.966.60.65421410.8620.9620.2720.7090.491100
1.96-26.70.5520730.8780.9670.2280.5970.505100
2-2.046.70.50821370.9110.9760.2110.5510.511100
2.04-2.086.60.39921170.9370.9840.1670.4340.515100
2.08-2.126.50.32621420.950.9870.1380.3540.518100
2.12-2.176.10.2920700.9630.9910.1270.3170.528100
2.17-2.236.40.2621610.9710.9930.1110.2830.542100
2.23-2.296.70.21720800.9760.9940.090.2360.563100
2.29-2.366.90.19621100.9810.9950.080.2120.577100
2.36-2.436.90.1721390.9870.9970.0690.1840.577100
2.43-2.526.80.15520970.9860.9970.0640.1680.625100
2.52-2.626.80.13721440.9890.9970.0560.1480.649100
2.62-2.746.50.12321250.9830.9960.0520.1340.681100
2.74-2.886.30.10321380.9910.9980.0450.1130.701100
2.88-3.066.90.08821100.9940.9990.0360.0950.731100
3.06-3.370.07521410.9960.9990.030.0810.773100
3.3-3.636.90.06221340.9970.9990.0250.0670.768100
3.63-4.166.30.05321600.9970.9990.0230.0570.762100
4.16-5.246.80.04921650.9970.9990.020.0530.746100
5.24-506.40.04822140.99810.020.0520.68399.1

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M66

4m66


Resolution: 1.93→23.84 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 1983 4.66 %
Rwork0.1813 --
obs0.1826 42581 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→23.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 52 225 4639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054545
X-RAY DIFFRACTIONf_angle_d0.86188
X-RAY DIFFRACTIONf_dihedral_angle_d14.9381700
X-RAY DIFFRACTIONf_chiral_restr0.049698
X-RAY DIFFRACTIONf_plane_restr0.006788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.30111590.26932807X-RAY DIFFRACTION97
1.98-2.030.2821530.22592873X-RAY DIFFRACTION100
2.03-2.090.24681300.19872869X-RAY DIFFRACTION100
2.09-2.160.25931380.19122888X-RAY DIFFRACTION100
2.16-2.230.2451250.19532917X-RAY DIFFRACTION100
2.23-2.320.23891250.18612926X-RAY DIFFRACTION100
2.32-2.430.25491310.18522873X-RAY DIFFRACTION100
2.43-2.560.25641250.19092928X-RAY DIFFRACTION100
2.56-2.720.22351350.18922907X-RAY DIFFRACTION100
2.72-2.930.2391630.20012861X-RAY DIFFRACTION100
2.93-3.220.22551470.19352892X-RAY DIFFRACTION100
3.22-3.680.20231760.17732894X-RAY DIFFRACTION100
3.68-4.640.16181570.15022921X-RAY DIFFRACTION100
4.64-23.840.15491190.16873042X-RAY DIFFRACTION100

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