SMTL ID : 6pls.1

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

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

TAU.6: 8 residues within 4Å: Chain A: F.87, R.89, S.153 Chain B: F.123, S.182, F.183, Y.226, T.228 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.183, A:S.153 Salt bridges: A:R.89 TAU.13: 8 residues within 4Å: Chain A: F.123, S.182, F.183, Y.226, T.228 Chain E: F.87, R.89, S.153 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:S.153, A:F.183 Salt bridges: E:R.89 TAU.26: 8 residues within 4Å: Chain B: F.87, R.89, S.153 Chain C: F.123, S.182, F.183, Y.226, T.228 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:F.183, B:S.153 Salt bridges: B:R.89 TAU.39: 8 residues within 4Å: Chain C: F.87, R.89, S.153 Chain D: F.123, S.182, F.183, Y.226, T.228 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:F.183, C:S.153 Salt bridges: C:R.89 TAU.52: 8 residues within 4Å: Chain D: F.87, R.89, S.153 Chain E: F.123, S.182, F.183, Y.226, T.228 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:S.153, E:F.183 Salt bridges: D:R.89

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

UNL.7: 2 residues within 4Å: Chain B: V.313 Ligands: UNL.21 Ligand excluded by PLIP UNL.8: 2 residues within 4Å: Chain A: I.253 Ligands: UNL.9 Ligand excluded by PLIP UNL.9: 4 residues within 4Å: Chain A: N.426, I.431, K.434 Ligands: UNL.8 Ligand excluded by PLIP UNL.10: 3 residues within 4Å: Chain A: V.264, W.267 Ligands: UNL.24 Ligand excluded by PLIP UNL.11: 1 residues within 4Å: Chain A: W.267 Ligand excluded by PLIP UNL.12: 1 residues within 4Å: Ligands: UNL.25 Ligand excluded by PLIP UNL.14: 5 residues within 4Å: Chain A: I.309, F.425, F.428, Y.433 Ligands: UNL.15 Ligand excluded by PLIP UNL.15: 3 residues within 4Å: Chain A: V.304 Ligands: UNL.14, UNL.65 Ligand excluded by PLIP UNL.16: 1 residues within 4Å: Chain A: L.420 Ligand excluded by PLIP UNL.17: 3 residues within 4Å: Chain A: L.316, F.418 Ligands: UNL.18 Ligand excluded by PLIP UNL.18: 3 residues within 4Å: Chain A: I.410 Ligands: UNL.17, UNL.68 Ligand excluded by PLIP UNL.19: 1 residues within 4Å: Ligands: UNL.70 Ligand excluded by PLIP UNL.20: 5 residues within 4Å: Chain B: I.309, F.425, F.428, Y.433 Ligands: UNL.21 Ligand excluded by PLIP UNL.21: 3 residues within 4Å: Chain B: V.304 Ligands: UNL.7, UNL.20 Ligand excluded by PLIP UNL.22: 1 residues within 4Å: Chain B: L.420 Ligand excluded by PLIP UNL.23: 3 residues within 4Å: Chain B: L.316, F.418 Ligands: UNL.24 Ligand excluded by PLIP UNL.24: 3 residues within 4Å: Chain B: I.410 Ligands: UNL.10, UNL.23 Ligand excluded by PLIP UNL.25: 1 residues within 4Å: Ligands: UNL.12 Ligand excluded by PLIP UNL.27: 2 residues within 4Å: Chain C: V.313 Ligands: UNL.34 Ligand excluded by PLIP UNL.28: 2 residues within 4Å: Chain B: I.253 Ligands: UNL.29 Ligand excluded by PLIP UNL.29: 4 residues within 4Å: Chain B: N.426, I.431, K.434 Ligands: UNL.28 Ligand excluded by PLIP UNL.30: 3 residues within 4Å: Chain B: V.264, W.267 Ligands: UNL.37 Ligand excluded by PLIP UNL.31: 1 residues within 4Å: Chain B: W.267 Ligand excluded by PLIP UNL.32: 1 residues within 4Å: Ligands: UNL.38 Ligand excluded by PLIP UNL.33: 5 residues within 4Å: Chain C: I.309, F.425, F.428, Y.433 Ligands: UNL.34 Ligand excluded by PLIP UNL.34: 3 residues within 4Å: Chain C: V.304 Ligands: UNL.27, UNL.33 Ligand excluded by PLIP UNL.35: 1 residues within 4Å: Chain C: L.420 Ligand excluded by PLIP UNL.36: 3 residues within 4Å: Chain C: L.316, F.418 Ligands: UNL.37 Ligand excluded by PLIP UNL.37: 3 residues within 4Å: Chain C: I.410 Ligands: UNL.30, UNL.36 Ligand excluded by PLIP UNL.38: 1 residues within 4Å: Ligands: UNL.32 Ligand excluded by PLIP UNL.40: 2 residues within 4Å: Chain D: V.313 Ligands: UNL.47 Ligand excluded by PLIP UNL.41: 2 residues within 4Å: Chain C: I.253 Ligands: UNL.42 Ligand excluded by PLIP UNL.42: 4 residues within 4Å: Chain C: N.426, I.431, K.434 Ligands: UNL.41 Ligand excluded by PLIP UNL.43: 3 residues within 4Å: Chain C: V.264, W.267 Ligands: UNL.50 Ligand excluded by PLIP UNL.44: 1 residues within 4Å: Chain C: W.267 Ligand excluded by PLIP UNL.45: 1 residues within 4Å: Ligands: UNL.51 Ligand excluded by PLIP UNL.46: 5 residues within 4Å: Chain D: I.309, F.425, F.428, Y.433 Ligands: UNL.47 Ligand excluded by PLIP UNL.47: 3 residues within 4Å: Chain D: V.304 Ligands: UNL.40, UNL.46 Ligand excluded by PLIP UNL.48: 1 residues within 4Å: Chain D: L.420 Ligand excluded by PLIP UNL.49: 3 residues within 4Å: Chain D: L.316, F.418 Ligands: UNL.50 Ligand excluded by PLIP UNL.50: 3 residues within 4Å: Chain D: I.410 Ligands: UNL.43, UNL.49 Ligand excluded by PLIP UNL.51: 1 residues within 4Å: Ligands: UNL.45 Ligand excluded by PLIP UNL.53: 2 residues within 4Å: Chain E: V.313 Ligands: UNL.60 Ligand excluded by PLIP UNL.54: 2 residues within 4Å: Chain D: I.253 Ligands: UNL.55 Ligand excluded by PLIP UNL.55: 4 residues within 4Å: Chain D: N.426, I.431, K.434 Ligands: UNL.54 Ligand excluded by PLIP UNL.56: 3 residues within 4Å: Chain D: V.264, W.267 Ligands: UNL.63 Ligand excluded by PLIP UNL.57: 1 residues within 4Å: Chain D: W.267 Ligand excluded by PLIP UNL.58: 1 residues within 4Å: Ligands: UNL.64 Ligand excluded by PLIP UNL.59: 5 residues within 4Å: Chain E: I.309, F.425, F.428, Y.433 Ligands: UNL.60 Ligand excluded by PLIP UNL.60: 3 residues within 4Å: Chain E: V.304 Ligands: UNL.53, UNL.59 Ligand excluded by PLIP UNL.61: 1 residues within 4Å: Chain E: L.420 Ligand excluded by PLIP UNL.62: 3 residues within 4Å: Chain E: L.316, F.418 Ligands: UNL.63 Ligand excluded by PLIP UNL.63: 3 residues within 4Å: Chain E: I.410 Ligands: UNL.56, UNL.62 Ligand excluded by PLIP UNL.64: 1 residues within 4Å: Ligands: UNL.58 Ligand excluded by PLIP UNL.65: 2 residues within 4Å: Chain A: V.313 Ligands: UNL.15 Ligand excluded by PLIP UNL.66: 2 residues within 4Å: Chain E: I.253 Ligands: UNL.67 Ligand excluded by PLIP UNL.67: 4 residues within 4Å: Chain E: N.426, I.431, K.434 Ligands: UNL.66 Ligand excluded by PLIP UNL.68: 3 residues within 4Å: Chain E: V.264, W.267 Ligands: UNL.18 Ligand excluded by PLIP UNL.69: 1 residues within 4Å: Chain E: W.267 Ligand excluded by PLIP UNL.70: 1 residues within 4Å: Ligands: UNL.19 Ligand excluded by 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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