SMTL ID : 6plv.1

CryoEM structure of zebra fish alpha-1 glycine receptor bound with GABA 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)

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

UNL.6: 4 residues within 4Å: Chain A: S.320, I.410, F.418 Ligands: UNL.7 Ligand excluded by PLIP UNL.7: 3 residues within 4Å: Chain A: S.320, I.410 Ligands: UNL.6 Ligand excluded by PLIP UNL.8: 1 residues within 4Å: Chain A: F.330 Ligand excluded by PLIP UNL.9: 2 residues within 4Å: Chain A: F.428, Y.433 Ligand excluded by PLIP UNL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.13: 2 residues within 4Å: Chain A: N.426 Ligands: UNL.17 Ligand excluded by PLIP UNL.14: 1 residues within 4Å: Chain B: F.330 Ligand excluded by PLIP UNL.15: 2 residues within 4Å: Chain A: I.249 Ligands: UNL.19 Ligand excluded by PLIP UNL.16: 1 residues within 4Å: Ligands: UNL.18 Ligand excluded by PLIP UNL.17: 3 residues within 4Å: Chain A: N.426, I.427 Ligands: UNL.13 Ligand excluded by PLIP UNL.18: 2 residues within 4Å: Chain A: W.267 Ligands: UNL.16 Ligand excluded by PLIP UNL.19: 1 residues within 4Å: Ligands: UNL.15 Ligand excluded by PLIP UNL.20: 4 residues within 4Å: Chain B: S.320, I.410, F.418 Ligands: UNL.21 Ligand excluded by PLIP UNL.21: 3 residues within 4Å: Chain B: S.320, I.410 Ligands: UNL.20 Ligand excluded by PLIP UNL.22: 2 residues within 4Å: Chain B: F.428, Y.433 Ligand excluded by PLIP UNL.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.26: 2 residues within 4Å: Chain B: N.426 Ligands: UNL.30 Ligand excluded by PLIP UNL.27: 1 residues within 4Å: Chain C: F.330 Ligand excluded by PLIP UNL.28: 2 residues within 4Å: Chain B: I.249 Ligands: UNL.32 Ligand excluded by PLIP UNL.29: 1 residues within 4Å: Ligands: UNL.31 Ligand excluded by PLIP UNL.30: 3 residues within 4Å: Chain B: N.426, I.427 Ligands: UNL.26 Ligand excluded by PLIP UNL.31: 2 residues within 4Å: Chain B: W.267 Ligands: UNL.29 Ligand excluded by PLIP UNL.32: 1 residues within 4Å: Ligands: UNL.28 Ligand excluded by PLIP UNL.33: 4 residues within 4Å: Chain C: S.320, I.410, F.418 Ligands: UNL.34 Ligand excluded by PLIP UNL.34: 3 residues within 4Å: Chain C: S.320, I.410 Ligands: UNL.33 Ligand excluded by PLIP UNL.35: 2 residues within 4Å: Chain C: F.428, Y.433 Ligand excluded by PLIP UNL.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.39: 2 residues within 4Å: Chain C: N.426 Ligands: UNL.43 Ligand excluded by PLIP UNL.40: 1 residues within 4Å: Chain D: F.330 Ligand excluded by PLIP UNL.41: 2 residues within 4Å: Chain C: I.249 Ligands: UNL.45 Ligand excluded by PLIP UNL.42: 1 residues within 4Å: Ligands: UNL.44 Ligand excluded by PLIP UNL.43: 3 residues within 4Å: Chain C: N.426, I.427 Ligands: UNL.39 Ligand excluded by PLIP UNL.44: 2 residues within 4Å: Chain C: W.267 Ligands: UNL.42 Ligand excluded by PLIP UNL.45: 1 residues within 4Å: Ligands: UNL.41 Ligand excluded by PLIP UNL.46: 4 residues within 4Å: Chain D: S.320, I.410, F.418 Ligands: UNL.47 Ligand excluded by PLIP UNL.47: 3 residues within 4Å: Chain D: S.320, I.410 Ligands: UNL.46 Ligand excluded by PLIP UNL.48: 2 residues within 4Å: Chain D: F.428, Y.433 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.52: 2 residues within 4Å: Chain D: N.426 Ligands: UNL.55 Ligand excluded by PLIP UNL.53: 2 residues within 4Å: Chain D: I.249 Ligands: UNL.57 Ligand excluded by PLIP UNL.54: 1 residues within 4Å: Ligands: UNL.56 Ligand excluded by PLIP UNL.55: 3 residues within 4Å: Chain D: N.426, I.427 Ligands: UNL.52 Ligand excluded by PLIP UNL.56: 2 residues within 4Å: Chain D: W.267 Ligands: UNL.54 Ligand excluded by PLIP UNL.57: 1 residues within 4Å: Ligands: UNL.53 Ligand excluded by PLIP UNL.59: 2 residues within 4Å: Chain E: N.426 Ligands: UNL.62 Ligand excluded by PLIP UNL.60: 2 residues within 4Å: Chain E: I.249 Ligands: UNL.64 Ligand excluded by PLIP UNL.61: 1 residues within 4Å: Ligands: UNL.63 Ligand excluded by PLIP UNL.62: 3 residues within 4Å: Chain E: N.426, I.427 Ligands: UNL.59 Ligand excluded by PLIP UNL.63: 2 residues within 4Å: Chain E: W.267 Ligands: UNL.61 Ligand excluded by PLIP UNL.64: 1 residues within 4Å: Ligands: UNL.60 Ligand excluded by PLIP UNL.65: 4 residues within 4Å: Chain E: S.320, I.410, F.418 Ligands: UNL.66 Ligand excluded by PLIP UNL.66: 3 residues within 4Å: Chain E: S.320, I.410 Ligands: UNL.65 Ligand excluded by PLIP UNL.67: 1 residues within 4Å: Chain E: F.330 Ligand excluded by PLIP UNL.68: 2 residues within 4Å: Chain E: F.428, Y.433 Ligand excluded by PLIP UNL.69: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.70: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

5 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.12: 10 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 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.87, A:L.141 Hydrogen bonds: A:S.153, B:S.182, B:T.228 Salt bridges: A:R.89 ABU.25: 10 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 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.87, B:L.141 Hydrogen bonds: B:S.153, C:S.182, C:T.228 Salt bridges: B:R.89 ABU.38: 10 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 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:S.182, D:T.228, C:S.153 Hydrophobic interactions: C:F.87, C:L.141 Salt bridges: C:R.89 ABU.51: 10 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 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:F.87, D:L.141 Hydrogen bonds: D:S.153, E:S.182, E:T.228 Salt bridges: D:R.89 ABU.58: 10 residues within 4Å: Chain A: F.123, E.181, S.182, F.183, Y.226, T.228 Chain E: F.87, R.89, L.141, S.153 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:F.87, E:L.141 Hydrogen bonds: E:S.153, A:S.182, A: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
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Glycine receptor subunit alphaZ1

Related Entries With Identical Sequence