SMTL ID : 6plt.1

CryoEM structure of zebra fish alpha-1 glycine receptor bound with taurine in nanodisc, closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

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

45 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.6: 2 residues within 4Å: Chain A: I.410, F.418 Ligand excluded by PLIP UNL.7: 2 residues within 4Å: Chain A: S.320, I.410 Ligand excluded by PLIP UNL.8: 1 residues within 4Å: Chain A: F.330 Ligand excluded by PLIP UNL.9: 1 residues within 4Å: Chain A: A.417 Ligand excluded by PLIP UNL.10: 1 residues within 4Å: Chain A: F.425 Ligand excluded by PLIP UNL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.13: 1 residues within 4Å: Chain A: I.249 Ligand excluded by PLIP UNL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.18: 1 residues within 4Å: Chain B: I.249 Ligand excluded by PLIP UNL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.21: 2 residues within 4Å: Chain B: I.410, F.418 Ligand excluded by PLIP UNL.22: 2 residues within 4Å: Chain B: S.320, I.410 Ligand excluded by PLIP UNL.23: 1 residues within 4Å: Chain B: F.330 Ligand excluded by PLIP UNL.24: 1 residues within 4Å: Chain B: A.417 Ligand excluded by PLIP UNL.25: 1 residues within 4Å: Chain B: F.425 Ligand excluded by PLIP UNL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.28: 1 residues within 4Å: Chain C: I.249 Ligand excluded by PLIP UNL.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.31: 2 residues within 4Å: Chain C: I.410, F.418 Ligand excluded by PLIP UNL.32: 2 residues within 4Å: Chain C: S.320, I.410 Ligand excluded by PLIP UNL.33: 1 residues within 4Å: Chain C: F.330 Ligand excluded by PLIP UNL.34: 1 residues within 4Å: Chain C: A.417 Ligand excluded by PLIP UNL.35: 1 residues within 4Å: Chain C: F.425 Ligand excluded by PLIP UNL.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.38: 1 residues within 4Å: Chain D: I.249 Ligand excluded by PLIP UNL.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.41: 2 residues within 4Å: Chain D: I.410, F.418 Ligand excluded by PLIP UNL.42: 2 residues within 4Å: Chain D: S.320, I.410 Ligand excluded by PLIP UNL.43: 1 residues within 4Å: Chain D: F.330 Ligand excluded by PLIP UNL.44: 1 residues within 4Å: Chain D: A.417 Ligand excluded by PLIP UNL.45: 1 residues within 4Å: Chain D: F.425 Ligand excluded by PLIP UNL.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.48: 1 residues within 4Å: Chain E: I.249 Ligand excluded by PLIP UNL.49: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.50: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.51: 2 residues within 4Å: Chain E: I.410, F.418 Ligand excluded by PLIP UNL.52: 2 residues within 4Å: Chain E: S.320, I.410 Ligand excluded by PLIP UNL.53: 1 residues within 4Å: Chain E: F.330 Ligand excluded by PLIP UNL.54: 1 residues within 4Å: Chain E: A.417 Ligand excluded by PLIP UNL.55: 1 residues within 4Å: Chain E: F.425 Ligand excluded by PLIP

5 x TAU: 2-AMINOETHANESULFONIC ACID(Non-covalent)

TAU.11: 8 residues within 4Å: Chain A: F.87, R.89, L.141, S.153 Chain E: F.183, Y.226, T.228, F.231 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:S.153, A:S.153, A:S.153, E:T.228, E:T.228 Salt bridges: A:R.89 TAU.16: 8 residues within 4Å: Chain A: F.183, Y.226, T.228, F.231 Chain B: F.87, R.89, L.141, S.153 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.153, B:S.153, B:S.153, A:T.228, A:T.228 Salt bridges: B:R.89 TAU.26: 8 residues within 4Å: Chain B: F.183, Y.226, T.228, F.231 Chain C: F.87, R.89, L.141, S.153 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.153, C:S.153, C:S.153, B:T.228, B:T.228 Salt bridges: C:R.89 TAU.36: 8 residues within 4Å: Chain C: F.183, Y.226, T.228, F.231 Chain D: F.87, R.89, L.141, S.153 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.153, D:S.153, D:S.153, C:T.228, C:T.228 Salt bridges: D:R.89 TAU.46: 8 residues within 4Å: Chain D: F.183, Y.226, T.228, F.231 Chain E: F.87, R.89, L.141, S.153 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:S.153, E:S.153, E:S.153, D:T.228, D:T.228 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

2021-01-06

Peptides

Glycine receptor subunit alphaZ1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
D

D
C

E
B

Membrane

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

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