SMTL ID : 9boy.1

Cryo-EM structure of human Glycine Receptor apha3-beta heteromer with glycine in nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 5 residues within 4Å: Chain A: N.31, P.35, P.36, N.38, I.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.38 NAG.4: 3 residues within 4Å: Chain B: N.31, P.36, N.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.36 NAG.6: 5 residues within 4Å: Chain C: P.35, P.36, N.38, I.167, E.169 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.35 Hydrogen bonds: C:N.38 NAG.8: 4 residues within 4Å: Chain D: N.31, P.35, P.36, N.38 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.31, D:P.36 NAG.10: 4 residues within 4Å: Chain E: F.189, I.190, N.218, T.220 No protein-ligand interaction detected (PLIP)

5 x GLY: GLYCINE(Non-covalent)

GLY.2: 8 residues within 4Å: Chain A: F.63, R.65, L.117, S.129 Chain E: F.180, Y.223, T.226, Y.229 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: E:F.180, E:T.226, A:S.129, G.2 Salt bridges: A:R.65 GLY.3: 4 residues within 4Å: Chain A: N.203, T.204 Chain B: K.67, L.127 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.67 GLY.5: 7 residues within 4Å: Chain B: F.159, Y.202, F.207 Chain C: F.63, R.65, L.117, S.129 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.129 Salt bridges: C:R.65 GLY.7: 7 residues within 4Å: Chain C: F.159, T.204, F.207 Chain D: F.63, R.65, L.117, S.129 5 PLIP interactions: 2 interactions with chain D, 2 Ligand-Ligand interactions, 1 interactions with chain C Hydrogen bonds: D:S.129, G.7, G.7, C:T.204 Salt bridges: D:R.65 GLY.9: 8 residues within 4Å: Chain D: F.159, Y.202, T.204, F.207 Chain E: F.82, R.84, L.138, S.150 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.150 Salt bridges: E:R.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., Cryo-EM structure of human Glycine Receptor apha3-beta heteromer with glycine in nanodisc. To Be Published

Release Date

2025-05-14

Peptides

Glycine receptor subunit alpha-3: ABCD
Glycine receptor subunit beta,Green fluorescent protein: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Glycine receptor subunit alpha-3

Glycine receptor subunit beta,Green fluorescent protein

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