SMTL ID : 6plr.1

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

Coordinates

PDB Format

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: 1 residues within 4Å: Chain B: S.302 Ligand excluded by PLIP UNL.7: 2 residues within 4Å: Chain A: I.253 Ligands: UNL.8 Ligand excluded by PLIP UNL.8: 5 residues within 4Å: Chain A: L.256, F.422, L.423, N.426 Ligands: UNL.7 Ligand excluded by PLIP UNL.9: 2 residues within 4Å: Chain B: L.323 Ligands: UNL.10 Ligand excluded by PLIP UNL.10: 2 residues within 4Å: Ligands: UNL.9, UNL.12 Ligand excluded by PLIP UNL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.12: 1 residues within 4Å: Ligands: UNL.10 Ligand excluded by PLIP UNL.14: 2 residues within 4Å: Chain A: F.428, Y.433 Ligand excluded by PLIP UNL.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.17: 3 residues within 4Å: Chain A: L.316, I.410, F.418 Ligand excluded by PLIP UNL.18: 1 residues within 4Å: Chain A: I.410 Ligand excluded by PLIP UNL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.21: 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: 3 residues within 4Å: Chain B: L.316, I.410, F.418 Ligand excluded by PLIP UNL.25: 2 residues within 4Å: Chain B: L.323, I.410 Ligand excluded by PLIP UNL.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.27: 1 residues within 4Å: Chain C: S.302 Ligand excluded by PLIP UNL.28: 2 residues within 4Å: Chain B: I.253 Ligands: UNL.29 Ligand excluded by PLIP UNL.29: 5 residues within 4Å: Chain B: L.256, F.422, L.423, N.426 Ligands: UNL.28 Ligand excluded by PLIP UNL.30: 2 residues within 4Å: Chain C: L.323 Ligands: UNL.31 Ligand excluded by PLIP UNL.31: 2 residues within 4Å: Ligands: UNL.30, UNL.33 Ligand excluded by PLIP UNL.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.33: 1 residues within 4Å: Ligands: UNL.31 Ligand excluded by PLIP UNL.35: 2 residues within 4Å: Chain C: F.428, Y.433 Ligand excluded by PLIP UNL.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.38: 2 residues within 4Å: Chain C: L.316, F.418 Ligand excluded by PLIP UNL.39: 1 residues within 4Å: Chain C: I.410 Ligand excluded by PLIP UNL.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.41: 1 residues within 4Å: Chain D: S.302 Ligand excluded by PLIP UNL.42: 2 residues within 4Å: Chain C: I.253 Ligands: UNL.43 Ligand excluded by PLIP UNL.43: 5 residues within 4Å: Chain C: L.256, F.422, L.423, N.426 Ligands: UNL.42 Ligand excluded by PLIP UNL.44: 2 residues within 4Å: Chain D: L.323 Ligands: UNL.45 Ligand excluded by PLIP UNL.45: 2 residues within 4Å: Ligands: UNL.44, UNL.47 Ligand excluded by PLIP UNL.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.47: 1 residues within 4Å: Ligands: UNL.45 Ligand excluded by PLIP UNL.49: 2 residues within 4Å: Chain D: F.428, Y.433 Ligand excluded by PLIP UNL.51: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.52: 2 residues within 4Å: Chain D: L.316, F.418 Ligand excluded by PLIP UNL.53: 1 residues within 4Å: Chain D: I.410 Ligand excluded by PLIP UNL.54: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.55: 1 residues within 4Å: Chain E: S.302 Ligand excluded by PLIP UNL.56: 2 residues within 4Å: Chain D: I.253 Ligands: UNL.57 Ligand excluded by PLIP UNL.57: 5 residues within 4Å: Chain D: L.256, F.422, L.423, N.426 Ligands: UNL.56 Ligand excluded by PLIP UNL.58: 2 residues within 4Å: Chain E: L.323 Ligands: UNL.59 Ligand excluded by PLIP UNL.59: 2 residues within 4Å: Ligands: UNL.58, UNL.61 Ligand excluded by PLIP UNL.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.61: 1 residues within 4Å: Ligands: UNL.59 Ligand excluded by PLIP UNL.63: 3 residues within 4Å: Chain E: I.309, F.428, Y.433 Ligand excluded by PLIP UNL.65: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.66: 3 residues within 4Å: Chain E: L.316, I.410, F.418 Ligand excluded by PLIP UNL.67: 2 residues within 4Å: Chain E: L.323, I.410 Ligand excluded by PLIP UNL.68: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.69: 1 residues within 4Å: Chain A: S.302 Ligand excluded by PLIP UNL.70: 2 residues within 4Å: Chain E: I.253 Ligands: UNL.71 Ligand excluded by PLIP UNL.71: 5 residues within 4Å: Chain E: L.256, F.422, L.423, N.426 Ligands: UNL.70 Ligand excluded by PLIP UNL.72: 2 residues within 4Å: Chain A: L.323 Ligands: UNL.73 Ligand excluded by PLIP UNL.73: 2 residues within 4Å: Ligands: UNL.72, UNL.75 Ligand excluded by PLIP UNL.74: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.75: 1 residues within 4Å: Ligands: UNL.73 Ligand excluded by PLIP

5 x GLY: GLYCINE(Non-covalent)

GLY.13: 9 residues within 4Å: Chain A: S.182, F.183, Y.226, T.228, F.231 Chain E: F.87, R.89, L.141, S.153 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.153, A:F.183, A:T.228 Salt bridges: E:R.89 GLY.20: 9 residues within 4Å: Chain A: F.87, R.89, L.141, S.153 Chain B: S.182, F.183, Y.226, T.228, F.231 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.153, B:F.183, B:T.228 Salt bridges: A:R.89 GLY.34: 9 residues within 4Å: Chain B: F.87, R.89, L.141, S.153 Chain C: S.182, F.183, Y.226, T.228, F.231 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:F.183, C:T.228, B:S.153 Salt bridges: B:R.89 GLY.48: 9 residues within 4Å: Chain C: F.87, R.89, L.141, S.153 Chain D: S.182, F.183, Y.226, T.228, F.231 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:F.183, D:T.228, C:S.153 Salt bridges: C:R.89 GLY.62: 9 residues within 4Å: Chain D: F.87, R.89, L.141, S.153 Chain E: S.182, F.183, Y.226, T.228, F.231 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:S.153, E:F.183, E:T.228 Salt bridges: D:R.89

5 x OCT: N-OCTANE(Non-functional Binders)

OCT.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.50: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.64: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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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