9E0V | pdb_00009e0v

GSDMD bound to a peptide

PDB DOI: https://doi.org/10.2210/pdb9E0V/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-19 Released: 2025-10-22
Deposition Author(s): Wang, R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.212 (Depositor), 0.209 (DCC)
R-Value Work:
0.200 (Depositor), 0.192 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Peptide binding at the Gasdermin D exosite reveals structural basis for targeting the site

Wang, R.

To be published.

Macromolecule Content

Total Structure Weight: 65.42 kDa
Atom Count: 1,759
Modeled Residue Count: 215
Deposited Residue Count: 601
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein, Gasdermin-D, C-terminal chimera	A	590	Homo sapiens	Mutation(s): 0 Gene Names: malE, b4034, JW3994, GSDMD, DFNA5L, GSDMDC1, FKSG10
UniProt & NIH Common Fund Data Resources
Find proteins for P57764 (Homo sapiens) Explore P57764 Go to UniProtKB: P57764
PHAROS: P57764 GTEx: ENSG00000104518
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P57764
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-CYS-ILE-LYS-LYS-ALA-VAL-6CW-PHE-LYS-CYS	B	11	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
6CW Query on 6CW	B	L-PEPTIDE LINKING	C₁₁ H₁₁ Cl N₂ O₂		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.212 (Depositor), 0.209 (DCC)
R-Value Work: 0.200 (Depositor), 0.192 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.575	α = 90
b = 47.575	β = 90
c = 194.717	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
pointless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release
Version 1.1: 2026-02-11
Changes: Data collection

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.