Cryo-EM structure of zebrafish TRPM5 in the presence of 5 mm calcium and 0.5 mm ndna

Structure

electron microscopy · 1 distinct chain · 62% helix, 8% strand (DSSP).

Ligands and binding sites

• YUS · N'-[(E)-(3,4-dimethoxyphenyl)methylidene]-2-(naphthalen-1-yl)acetohydrazide · ligand · 4 copies · chains A, D, B, C
• YUV · (25R)-14beta,17beta-spirost-5-en-3beta-ol · ligand · 4 copies · chains A, B, C, D
• YUY · (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
• CA · Calcium ion · metal · 8 copies · chains A, B, C, D

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.

Interfaces

6 interfaces between chains.

• A–D · 3305 Ų buried · 17 hydrogen bonds · protein-protein
• A–B · 3300 Ų buried · 17 hydrogen bonds · protein-protein
• B–C · 3299 Ų buried · 17 hydrogen bonds · protein-protein
• C–D · 3296 Ų buried · 17 hydrogen bonds · protein-protein
• A–C · 67 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan (N-glycosylation).

Compared structures

• 7MBV · Cryo-EM structure of zebrafish TRPM5 in the presence of 5 mM calcium and 0.5 mM NDNA · the same entry in another collection · chain A against A, TM-score 1.00

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 S5UH55
• Elsewhere: RCSB PDB 7MBV · PDBe 7MBV · UniProt S5UH55