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- PDB-9lfv: Crystal structure of mouse RIP3 kinase domain complexed with LK01004 -

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Basic information

Entry
Database: PDB / ID: 9lfv
TitleCrystal structure of mouse RIP3 kinase domain complexed with LK01004
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 necroptotic cell death / IKK complex recruitment mediated by RIP1 / regulation of adaptive immune response / regulation of activated T cell proliferation ...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 necroptotic cell death / IKK complex recruitment mediated by RIP1 / regulation of adaptive immune response / regulation of activated T cell proliferation / regulation of type II interferon production / programmed necrotic cell death / necroptotic signaling pathway / TRP channels / activation of protein kinase activity / positive regulation of necroptotic process / non-canonical NF-kappaB signal transduction / regulation of reactive oxygen species metabolic process / T cell homeostasis / necroptotic process / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / 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 / 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: 2.78 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
DepositionJan 9, 2025Deposition 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
C: Receptor-interacting serine/threonine-protein kinase 3
D: Receptor-interacting serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,7569
Polymers144,8534
Non-polymers1,9035
Water25214
1
A: Receptor-interacting serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9743
Polymers36,2131
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-interacting serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5942
Polymers36,2131
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Receptor-interacting serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5942
Polymers36,2131
Non-polymers3811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Receptor-interacting serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5942
Polymers36,2131
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.662, 94.662, 122.210
Angle α, β, γ (deg.)90.00, 90.98, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4
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-A1EJO / 3-[2-[(2~{S})-butan-2-yl]-1,3-benzothiazol-5-yl]-1-~{tert}-butyl-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 380.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N6S
#3: Chemical
ChemComp-A1EJP / 3-[2-[(2~{R})-butan-2-yl]-1,3-benzothiazol-5-yl]-1-~{tert}-butyl-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 380.510 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.05M magnesium formate, 20% PEG3350, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.78→74.83 Å / Num. obs: 32505 / % possible obs: 100 % / Redundancy: 5.8 % / CC1/2: 0.975 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.087 / Rrim(I) all: 0.208 / Χ2: 0.99 / Net I/σ(I): 6.8 / Num. measured all: 187746
Reflection shellResolution: 2.78→2.93 Å / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 2.011 / Num. measured all: 27424 / Num. unique obs: 4687 / CC1/2: 0.485 / Rpim(I) all: 0.904 / Rrim(I) all: 2.209 / Χ2: 0.94 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→61.1 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 1517 4.72 %
Rwork0.247 --
obs0.2487 32167 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→61.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7396 0 108 14 7518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067722
X-RAY DIFFRACTIONf_angle_d0.97610605
X-RAY DIFFRACTIONf_dihedral_angle_d12.9892675
X-RAY DIFFRACTIONf_chiral_restr0.0541237
X-RAY DIFFRACTIONf_plane_restr0.011354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.870.33121340.30882729X-RAY DIFFRACTION99
2.87-2.980.34331170.31362857X-RAY DIFFRACTION100
2.98-3.10.37111210.29292753X-RAY DIFFRACTION100
3.1-3.240.35151190.29162835X-RAY DIFFRACTION100
3.24-3.410.30221610.26882781X-RAY DIFFRACTION100
3.41-3.620.311290.26462791X-RAY DIFFRACTION100
3.62-3.90.36221380.30562654X-RAY DIFFRACTION94
3.9-4.290.27321370.21612802X-RAY DIFFRACTION99
4.29-4.910.22141490.19132808X-RAY DIFFRACTION100
4.91-6.190.25761450.24522834X-RAY DIFFRACTION100
6.19-61.10.24551670.22552806X-RAY DIFFRACTION98

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