5NH1

Structure of the C-terminal domain of human Gasdermin D

PDB DOI: https://doi.org/10.2210/pdb5NH1/pdb

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

Deposited: 2017-03-21 Released: 2017-09-20
Deposition Author(s): Anton, L., Sborgi, L., Hiller, S., Broz, P., Maier, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.264
R-Value Work: 0.231
R-Value Observed: 0.233

wwPDB Validation 3D Report Full Report

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

Literature

Insights into Gasdermin D activation from the crystal structure of its C-terminal domain

Anton, L., Sborgi, L., Hiller, S., Broz, P., Maier, T.

(2017) Biorxiv

DOI: https://doi.org/10.1101/187211

Macromolecule Content

Total Structure Weight: 22.17 kDa
Atom Count: 1,656
Modelled Residue Count: 199
Deposited Residue Count: 207
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	207	Homo sapiens	Mutation(s): 0 Gene Names: 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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.264
R-Value Work: 0.231
R-Value Observed: 0.233
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.73	α = 90
b = 47.98	β = 90
c = 37.65	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-09-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-09-20
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.