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 1.0 of the entry. See complete history.

Literature

Improved structure of mouse Gasdermin D

De Colibus, L., Biasutto, A., Jazayeri, A., Duerr, K.L.

To be published.

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

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(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 C [auth A] SDF format, chain E [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain G [auth B]	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 F [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [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]