9HJP | pdb_00009hjp

Improved structure of mouse Gasdermin D

PDB DOI: https://doi.org/10.2210/pdb9HJP/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli 0.1288
Mutation(s): No

Deposited: 2024-11-29 Released: 2025-10-01
Deposition Author(s): De Colibus, L., Biasutto, A., Jazayeri, A., Duerr, K.L.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.260 (Depositor), 0.274 (DCC)
R-Value Work:
0.239 (Depositor), 0.237 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Improved structure of mouse gasdermin D: a new blueprint for structure-based drug design.

De Colibus, L., Ludzia, P., Biasutto, A., Pica, A., Hopper, J.T.S., Jazayeri, A., Durr, K.L.

(2025) Acta Crystallogr F Struct Biol Commun 81: 408-415

PubMed: 40906124 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X25007149
Primary Citation Related Structures:
9HJP

PubMed Abstract:
Gasdermin D (GSDMD) is a protein that has gained significant attention in recent years due to its crucial role in inflammatory cell death, particularly pyroptosis. Pyroptosis is a highly inflammatory form of programmed cell death that is triggered by various microbial infections and sterile inflammatory stimuli. GSDMD acts as an executioner molecule in this process, leading to the release of pro-inflammatory cytokines and amplifying the immune response. Here, we present a higher resolution, significantly improved apo crystal structure of the deposited mouse structure model that will be beneficial for structure-based drug-design approaches towards this important pharmacological target.

Organizational Affiliation

OMass Therapeutics, Building 4000, Chancellor Court, John Smith Drive, Oxford Business Park, ARC, Oxford OX4 2GX, United Kingdom.

Macromolecule Content

Total Structure Weight: 99.85 kDa
Atom Count: 6,217
Modeled Residue Count: 790
Deposited Residue Count: 904
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gasdermin-D	A, B	452	Mus musculus	Mutation(s): 0 Gene Names: Gsdmd, Gsdmdc1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D8T2 (Mus musculus) Explore Q9D8T2 Go to UniProtKB: Q9D8T2
IMPC: MGI:1916396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9D8T2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE8 Query on PE8 Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C₁₆ H₃₄ O₉ GLZWNFNQMJAZGY-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B] Focus chain G [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth B]	F [auth B], H [auth B], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain F [auth B] Focus chain H [auth B] Focus chain I [auth B]