SMTL ID : 6plu.1

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

ABU.6: 10 residues within 4Å: Chain A: F.87, R.89, S.153 Chain B: F.123, E.181, S.182, F.183, Y.226, T.228, F.231 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.226, B:F.231, A:F.87 Hydrogen bonds: B:S.182, B:Y.226, B:T.228, A:S.153 Salt bridges: A:R.89 ABU.12: 10 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, S.153 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:Y.226, A:F.231, E:F.87 Hydrogen bonds: A:S.182, A:Y.226, A:T.228, E:S.153 Salt bridges: E:R.89 ABU.29: 10 residues within 4Å: Chain B: F.87, R.89, S.153 Chain C: F.123, E.181, S.182, F.183, Y.226, T.228, F.231 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:F.87, C:Y.226, C:F.231 Hydrogen bonds: B:S.153, C:S.182, C:Y.226, C:T.228 Salt bridges: B:R.89 ABU.43: 10 residues within 4Å: Chain C: F.87, R.89, S.153 Chain D: F.123, E.181, S.182, F.183, Y.226, T.228, F.231 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.87, D:Y.226, D:F.231 Hydrogen bonds: C:S.153, D:S.182, D:Y.226, D:T.228 Salt bridges: C:R.89 ABU.57: 10 residues within 4Å: Chain D: F.87, R.89, S.153 Chain E: F.123, E.181, S.182, F.183, Y.226, T.228, F.231 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:Y.226, E:F.231, D:F.87 Hydrogen bonds: E:S.182, E:Y.226, E:T.228, D:S.153 Salt bridges: D:R.89

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

UNL.7: 1 residues within 4Å: Ligands: UNL.8 Ligand excluded by PLIP UNL.8: 3 residues within 4Å: Chain A: N.426, K.434 Ligands: UNL.7 Ligand excluded by PLIP UNL.9: 5 residues within 4Å: Chain A: I.260, V.264 Chain B: L.323, A.326, F.330 Ligand excluded by PLIP UNL.10: 1 residues within 4Å: Chain A: W.267 Ligand excluded by PLIP UNL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.13: 3 residues within 4Å: Chain A: F.425, F.428 Ligands: UNL.20 Ligand excluded by PLIP UNL.14: 2 residues within 4Å: Ligands: UNL.15, UNL.20 Ligand excluded by PLIP UNL.15: 2 residues within 4Å: Chain A: S.302 Ligands: UNL.14 Ligand excluded by PLIP UNL.16: 1 residues within 4Å: Chain A: V.416 Ligand excluded by PLIP UNL.17: 3 residues within 4Å: Chain A: I.410, F.418 Ligands: UNL.18 Ligand excluded by PLIP UNL.18: 2 residues within 4Å: Chain A: L.323 Ligands: UNL.17 Ligand excluded by PLIP UNL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.20: 2 residues within 4Å: Ligands: UNL.13, UNL.14 Ligand excluded by PLIP UNL.21: 3 residues within 4Å: Chain B: F.425, F.428 Ligands: UNL.28 Ligand excluded by PLIP UNL.22: 2 residues within 4Å: Ligands: UNL.23, UNL.28 Ligand excluded by PLIP UNL.23: 2 residues within 4Å: Chain B: S.302 Ligands: UNL.22 Ligand excluded by PLIP UNL.24: 1 residues within 4Å: Chain B: V.416 Ligand excluded by PLIP UNL.25: 3 residues within 4Å: Chain B: I.410, F.418 Ligands: UNL.26 Ligand excluded by PLIP UNL.26: 2 residues within 4Å: Chain B: L.323 Ligands: UNL.25 Ligand excluded by PLIP UNL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.28: 2 residues within 4Å: Ligands: UNL.21, UNL.22 Ligand excluded by PLIP UNL.30: 1 residues within 4Å: Ligands: UNL.31 Ligand excluded by PLIP UNL.31: 3 residues within 4Å: Chain B: N.426, K.434 Ligands: UNL.30 Ligand excluded by PLIP UNL.32: 5 residues within 4Å: Chain B: I.260, V.264 Chain C: L.323, A.326, F.330 Ligand excluded by PLIP UNL.33: 1 residues within 4Å: Chain B: W.267 Ligand excluded by PLIP UNL.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.35: 3 residues within 4Å: Chain C: F.425, F.428 Ligands: UNL.42 Ligand excluded by PLIP UNL.36: 2 residues within 4Å: Ligands: UNL.37, UNL.42 Ligand excluded by PLIP UNL.37: 2 residues within 4Å: Chain C: S.302 Ligands: UNL.36 Ligand excluded by PLIP UNL.38: 1 residues within 4Å: Chain C: V.416 Ligand excluded by PLIP UNL.39: 3 residues within 4Å: Chain C: I.410, F.418 Ligands: UNL.40 Ligand excluded by PLIP UNL.40: 2 residues within 4Å: Chain C: L.323 Ligands: UNL.39 Ligand excluded by PLIP UNL.41: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.42: 2 residues within 4Å: Ligands: UNL.35, UNL.36 Ligand excluded by PLIP UNL.44: 1 residues within 4Å: Ligands: UNL.45 Ligand excluded by PLIP UNL.45: 3 residues within 4Å: Chain C: N.426, K.434 Ligands: UNL.44 Ligand excluded by PLIP UNL.46: 5 residues within 4Å: Chain C: I.260, V.264 Chain D: L.323, A.326, F.330 Ligand excluded by PLIP UNL.47: 1 residues within 4Å: Chain C: W.267 Ligand excluded by PLIP UNL.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.49: 3 residues within 4Å: Chain D: F.425, F.428 Ligands: UNL.56 Ligand excluded by PLIP UNL.50: 2 residues within 4Å: Ligands: UNL.51, UNL.56 Ligand excluded by PLIP UNL.51: 2 residues within 4Å: Chain D: S.302 Ligands: UNL.50 Ligand excluded by PLIP UNL.52: 1 residues within 4Å: Chain D: V.416 Ligand excluded by PLIP UNL.53: 3 residues within 4Å: Chain D: I.410, F.418 Ligands: UNL.54 Ligand excluded by PLIP UNL.54: 2 residues within 4Å: Chain D: L.323 Ligands: UNL.53 Ligand excluded by PLIP UNL.55: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.56: 2 residues within 4Å: Ligands: UNL.49, UNL.50 Ligand excluded by PLIP UNL.58: 1 residues within 4Å: Ligands: UNL.59 Ligand excluded by PLIP UNL.59: 3 residues within 4Å: Chain D: N.426, K.434 Ligands: UNL.58 Ligand excluded by PLIP UNL.60: 5 residues within 4Å: Chain D: I.260, V.264 Chain E: L.323, A.326, F.330 Ligand excluded by PLIP UNL.61: 1 residues within 4Å: Chain D: W.267 Ligand excluded by PLIP UNL.62: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.63: 3 residues within 4Å: Chain E: F.425, F.428 Ligands: UNL.70 Ligand excluded by PLIP UNL.64: 2 residues within 4Å: Ligands: UNL.65, UNL.70 Ligand excluded by PLIP UNL.65: 2 residues within 4Å: Chain E: S.302 Ligands: UNL.64 Ligand excluded by PLIP UNL.66: 1 residues within 4Å: Chain E: V.416 Ligand excluded by PLIP UNL.67: 3 residues within 4Å: Chain E: I.410, F.418 Ligands: UNL.68 Ligand excluded by PLIP UNL.68: 2 residues within 4Å: Chain E: L.323 Ligands: UNL.67 Ligand excluded by PLIP UNL.69: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.70: 2 residues within 4Å: Ligands: UNL.63, UNL.64 Ligand excluded by PLIP UNL.71: 1 residues within 4Å: Ligands: UNL.72 Ligand excluded by PLIP UNL.72: 3 residues within 4Å: Chain E: N.426, K.434 Ligands: UNL.71 Ligand excluded by PLIP UNL.73: 5 residues within 4Å: Chain A: L.323, A.326, F.330 Chain E: I.260, V.264 Ligand excluded by PLIP UNL.74: 1 residues within 4Å: Chain E: W.267 Ligand excluded by PLIP UNL.75: 0 residues within 4Å: (No contacts) 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.
Show / Hide

Glycine receptor subunit alphaZ1

Related Entries With Identical Sequence