SMTL ID : 6plx.1

CryoEM structure of zebra fish alpha-1 glycine receptor bound with GABA in SMA, desensitized 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 ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.6: 10 residues within 4Å: Chain A: E.181, S.182, F.183, Y.226, T.228, F.231 Chain E: F.87, R.89, L.141, S.153 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:F.87, A:F.183, A:Y.226 Hydrogen bonds: E:S.153, A:E.181 Salt bridges: E:R.89 ABU.7: 10 residues within 4Å: Chain A: F.87, R.89, L.141, S.153 Chain B: E.181, S.182, F.183, Y.226, T.228, F.231 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.87, B:F.183, B:Y.226 Hydrogen bonds: A:S.153, B:E.181 Salt bridges: A:R.89 ABU.8: 10 residues within 4Å: Chain B: F.87, R.89, L.141, S.153 Chain C: E.181, S.182, F.183, Y.226, T.228, F.231 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.87, C:F.183, C:Y.226 Hydrogen bonds: B:S.153, C:E.181 Salt bridges: B:R.89 ABU.9: 10 residues within 4Å: Chain C: F.87, R.89, L.141, S.153 Chain D: E.181, S.182, F.183, Y.226, T.228, F.231 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.87, D:F.183, D:Y.226 Hydrogen bonds: C:S.153, D:E.181 Salt bridges: C:R.89 ABU.10: 10 residues within 4Å: Chain D: F.87, R.89, L.141, S.153 Chain E: E.181, S.182, F.183, Y.226, T.228, F.231 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.87, E:F.183, E:Y.226 Hydrogen bonds: D:S.153, E:E.181 Salt bridges: D: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

2021-01-06

Peptides

Glycine receptor subunit alphaZ1: ABCDE

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 alphaZ1

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