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Gasdermin-B C-terminal domain containing the polymorphism residues GLY299:PRO306 fused to maltose binding protein

Analyse Gasdermin-B C-terminal domain containing the polymorphism residues… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TJ4
Type: protein
Length: 5,462 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein
UniProt: A0A178SBV6, Q8TAX9
Ligands: GLC, NA
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 10 distinct chains · 51% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein	protein	553	50% helix, 14% strand	A0A178SBV6, Q8TAX9
B	Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein	protein	554	50% helix, 15% strand	A0A178SBV6, Q8TAX9
C	Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein	protein	554	50% helix, 15% strand	A0A178SBV6, Q8TAX9
D	Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein	protein	541	52% helix, 15% strand	A0A178SBV6, Q8TAX9
E	Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein	protein	556	50% helix, 14% strand	A0A178SBV6, Q8TAX9
F	Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein	protein	541	52% helix, 15% strand	A0A178SBV6, Q8TAX9
G	Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein	protein	543	52% helix, 15% strand	A0A178SBV6, Q8TAX9
H	Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein	protein	537	52% helix, 15% strand	A0A178SBV6, Q8TAX9
I	Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein	protein	535	52% helix, 15% strand	A0A178SBV6, Q8TAX9
J	Sugar ABC transporter substrate-binding PROTEIN,GASDERMIN-B fusion protein	protein	548	51% helix, 15% strand	A0A178SBV6, Q8TAX9

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 20 copies · chains A, B, C, D, E, F, G, H, I, J
NA · Sodium ion · metal · 2 copies · chains B, C, A, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	977	0.82	0.83	96	empty
2	1156	0.82	0.83	98	empty
3	931	0.79	0.81	86	empty
4	537	0.77	0.84	54	GLC
5	286	0.74	0.87	32	GLC

Interfaces

14 interfaces between chains.

A–C · 2184 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 676 Å² buried · 5 hydrogen bonds · protein-protein
B–H · 616 Å² buried · 2 hydrogen bonds · protein-protein
A–E · 585 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 451 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5TJ4 · Gasdermin-B C-terminal domain containing the polymorphism residues Gly299:Pro306 fused to… · the same entry in another collection · chain J against J, TM-score 1.00
Q8TAX9 · AlphaFold monomer V2.0 prediction for gasdermin-B (Q8TAX9) · a predicted model of the same protein · chain C against A, TM-score 0.33

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 A0A178SBV6
Every structure of UniProt Q8TAX9
Elsewhere: RCSB PDB 5TJ4 · PDBe 5TJ4 · UniProt A0A178SBV6 · UniProt Q8TAX9

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