9LVG | pdb_00009lvg

Crystal structure of the mouse RIP3 kinase domain in complexed with Robinetin

PDB DOI: https://doi.org/10.2210/pdb9LVG/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-02-12 Released: 2025-05-07
Deposition Author(s): Xie, H., Su, H.X., Li, M.J., Xu, Y.C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 ?
R-Value Free:
0.236 (Depositor), 0.241 (DCC)
R-Value Work:
0.217 (Depositor), 0.223 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Identification of RIPK3 as a target of flavonoids for anti-necroptosis in vitro

Xie, H., Su, H.X., Li, M.J., Xu, Y.C.

(2025) Bioorg Chem

Macromolecule Content

Total Structure Weight: 73.03 kDa
Atom Count: 4,028
Modelled Residue Count: 518
Deposited Residue Count: 650
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 3	A, B	325	Mus musculus	Mutation(s): 0 Gene Names: Ripk3, Rip3 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QZL0 (Mus musculus) Explore Q9QZL0 Go to UniProtKB: Q9QZL0
IMPC: MGI:2154952
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9QZL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LKR (Subject of Investigation/LOI) Query on LKR Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	3,7-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]chromen-4-one C₁₅ H₁₀ O₇ SOEDEYVDCDYMMH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 ?
R-Value Free: 0.236 (Depositor), 0.241 (DCC)
R-Value Work: 0.217 (Depositor), 0.223 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 154.936	α = 90
b = 51.355	β = 132.57
c = 106.188	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	China	--

Revision History (Full details and data files)

Version 1.0: 2025-05-07
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.