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- PDB-9lfw: Crystal structure of mouse RIP3 kinase domain(R69H) complexed wit... -

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Basic information

Entry
Database: PDB / ID: 9lfw
TitleCrystal structure of mouse RIP3 kinase domain(R69H) complexed with LK01003
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: 1.59 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6462
Polymers36,1941
Non-polymers4521
Water3,621201
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)48.572, 64.785, 92.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 36194.281 Da / Num. of mol.: 1 / Mutation: C110A, R69H
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-A1D97 / 2-cyclopentyl-~{N}-(6-propan-2-ylsulfonylquinolin-4-yl)-1,3-benzothiazol-5-amine


Mass: 451.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25N3O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium acetate, 0.1 M MES, 30% v/v Glycerol ethoxylate, pH 6.5

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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: Mar 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.59→53.01 Å / Num. obs: 39200 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.07 / Rrim(I) all: 0.14 / Χ2: 0.84 / Net I/σ(I): 8.4
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 5.2 % / Rmerge(I) obs: 2.069 / Num. unique obs: 5706 / CC1/2: 0.432 / Rpim(I) all: 1.473 / Rrim(I) all: 2.554 / Χ2: 0.68

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→46.11 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 1963 5.01 %
Rwork0.2021 --
obs0.2039 39200 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 31 201 2483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062347
X-RAY DIFFRACTIONf_angle_d0.863203
X-RAY DIFFRACTIONf_dihedral_angle_d18.526873
X-RAY DIFFRACTIONf_chiral_restr0.052367
X-RAY DIFFRACTIONf_plane_restr0.006404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.43781260.39122393X-RAY DIFFRACTION91
1.63-1.680.42971400.36352568X-RAY DIFFRACTION97
1.68-1.730.38451620.32062589X-RAY DIFFRACTION99
1.73-1.780.29371210.28372642X-RAY DIFFRACTION99
1.78-1.850.30771350.24162666X-RAY DIFFRACTION100
1.85-1.920.26981400.22872657X-RAY DIFFRACTION100
1.92-2.010.25671460.20762657X-RAY DIFFRACTION100
2.01-2.110.24551270.18712666X-RAY DIFFRACTION100
2.11-2.250.22511280.18392709X-RAY DIFFRACTION100
2.25-2.420.23471370.19462679X-RAY DIFFRACTION100
2.42-2.660.28841550.20522678X-RAY DIFFRACTION100
2.66-3.050.26051300.1992736X-RAY DIFFRACTION100
3.05-3.840.21141600.17872728X-RAY DIFFRACTION100
3.84-46.110.17191560.17122869X-RAY DIFFRACTION100

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