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Crystal structure of the murine gasdermin D C-terminal domain

Analyse Crystal structure of the murine gasdermin D C-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AO3
Type: protein
Length: 793 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gasdermin-D
UniProt: Q9D8T2
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gasdermin-D	protein	199	65% helix, 6% strand	Q9D8T2
B, D	Gasdermin-D	protein	198	64% helix, 6% strand	Q9D8T2
C	Gasdermin-D	protein	198	64% helix, 6% strand	Q9D8T2

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	696	0.68	0.76	39	empty
2	570	0.64	0.75	38	empty
3	189	0.42	0.73	30	empty
4	74	0.30	0.73	15	empty
5	53	0.28	0.74	18	empty

Interfaces

4 interfaces between chains.

C–D · 944 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 917 Å² buried · 1 hydrogen bond · protein-protein
B–C · 276 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 21 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6AO3 · Crystal structure of the murine gasdermin D C-terminal domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9D8T2 · AlphaFold monomer V2.0 prediction for gasdermin-D (Q9D8T2) · a predicted model of the same protein · chain C against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9D8T2
Elsewhere: RCSB PDB 6AO3 · PDBe 6AO3 · UniProt Q9D8T2

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