5NH1 | pdb_00005nh1

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 22.17 kDa 
• Atom Count: 1,656 
• Modeled Residue Count: 199 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

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

Entry History 

Deposition Data

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

Revision History  

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