Full length glycine receptor reconstituted in lipid nanodisc in GLY/IVM-conformation (state-3)

Structure

electron microscopy · 1 distinct chain · 37% helix, 27% strand (DSSP).

Ligands and binding sites

• GLY · Glycine · ligand · 5 copies · chains A, E, B, C, D
• IVM · (2ae,4e,5's,6s,6'r,7s,8e,11r,13r,15s,17ar,20r,20ar, 20BS)-6'-[(2S)-butan-2-yl]-20,20B-dihydroxy-5',6,8,19-tetramethyl-17-oxo-3',4',5',6,6',10,11,14,15,17,17A, 20,20A,20B-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacyclooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside · ligand · 5 copies · chains A, B, E, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, E, C, B, 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, 18 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 2514 Ų buried · 16 hydrogen bonds · protein-protein
• C–D · 2480 Ų buried · 15 hydrogen bonds · protein-protein
• E–D · 2475 Ų buried · 14 hydrogen bonds · protein-protein
• C–B · 2449 Ų buried · 14 hydrogen bonds · protein-protein
• A–E · 2401 Ų buried · 12 hydrogen bonds · protein-protein

Compared structures

• 6VM3 · Full length Glycine receptor reconstituted in lipid nanodisc in Gly/IVM-conformation… · the same entry in another collection · chain D against D, TM-score 1.00
• O93430 · AlphaFold monomer V2.0 prediction for glycine receptor subunit ALPHAZ1 (O93430) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 O93430
• Elsewhere: RCSB PDB 6VM3 · PDBe 6VM3 · UniProt O93430