SMTL ID : 6pm6.1

CryoEM structure of zebra fish alpha-1 glycine receptor bound with Glycine in SMA, open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: N.55, P.59, P.60, N.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 4 residues within 4Å: Chain B: N.55, P.59, P.60, N.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain C: N.55, P.59, P.60, N.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 4 residues within 4Å: Chain D: N.55, P.59, P.60, N.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain E: N.55, P.59, P.60, N.62 No protein-ligand interaction detected (PLIP)

5 x GLY: GLYCINE(Non-covalent)

GLY.6: 8 residues within 4Å: Chain A: F.87, R.89, L.141, S.153 Chain C: S.182, F.183, T.228, F.231 5 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: G.6, G.6, A:S.153, C:S.182 Salt bridges: A:R.89 GLY.7: 7 residues within 4Å: Chain B: F.87, R.89, L.141, S.153 Chain E: F.183, T.228, F.231 5 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain B, 1 interactions with chain E Hydrogen bonds: G.7, G.7, B:S.153, E:S.182 Salt bridges: B:R.89 GLY.8: 8 residues within 4Å: Chain C: F.87, R.89, L.141, S.153 Chain D: S.182, F.183, T.228, F.231 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: C:S.153, D:S.182, G.8, G.8 Salt bridges: C:R.89 GLY.9: 7 residues within 4Å: Chain B: F.183, T.228, F.231 Chain D: F.87, R.89, L.141, S.153 5 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: G.9, G.9, D:S.153, B:S.182 Salt bridges: D:R.89 GLY.10: 8 residues within 4Å: Chain A: S.182, F.183, T.228, F.231 Chain E: F.87, R.89, L.141, S.153 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: E:S.153, A:S.182, G.10, G.10 Salt bridges: E:R.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, J. et al., Mechanism of gating and partial agonist action in the glycine receptor. Cell (2021)

Release Date

2021-02-10

Peptides

Glycine receptor subunit alphaZ1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

E
E

Membrane

We predict this structure to be a membrane protein.
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Glycine receptor subunit alphaZ1

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