SMTL ID : 6plw.1

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

ABU.6: 11 residues within 4Å: Chain A: F.87, R.89, L.141, S.153 Chain B: F.123, E.181, S.182, F.183, Y.226, T.228, F.231 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.141, B:F.183, B:F.231 Hydrogen bonds: A:S.153, B:E.181, B:S.182 Salt bridges: A:R.89 ABU.7: 11 residues within 4Å: Chain B: F.87, R.89, L.141, S.153 Chain C: F.123, E.181, S.182, F.183, Y.226, T.228, F.231 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.183, C:F.231, B:L.141 Hydrogen bonds: C:E.181, C:S.182, B:S.153 Salt bridges: B:R.89 ABU.8: 11 residues within 4Å: Chain C: F.87, R.89, L.141, S.153 Chain D: F.123, E.181, S.182, F.183, Y.226, T.228, F.231 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.183, D:F.231, C:L.141 Hydrogen bonds: D:E.181, D:S.182, C:S.153 Salt bridges: C:R.89 ABU.9: 11 residues within 4Å: Chain D: F.87, R.89, L.141, S.153 Chain E: F.123, E.181, S.182, F.183, Y.226, T.228, F.231 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:L.141, E:F.183, E:F.231 Hydrogen bonds: D:S.153, E:E.181, E:S.182 Salt bridges: D:R.89 ABU.10: 11 residues within 4Å: Chain A: F.123, E.181, S.182, F.183, Y.226, T.228, F.231 Chain E: F.87, R.89, L.141, S.153 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:F.183, A:F.231, E:L.141 Hydrogen bonds: A:E.181, A:S.182, E:S.153 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
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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