SMTL ID : 9bu2.1

Homomeric alpha3 glycine receptor in the presence of 1 mM glycine at pH 6.4 in a 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.64, P.68, P.69, N.71 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.64, P.68, P.69, N.71 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.64, P.68, P.69, N.71 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: N.64, P.68, P.69, N.71 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain E: N.64, P.68, P.69, N.71 No protein-ligand interaction detected (PLIP)

5 x GLY: GLYCINE(Non-covalent)

GLY.6: 7 residues within 4Å: Chain A: F.192, Y.235, T.237, F.240 Chain B: R.98, L.150, S.162 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.162, A:T.237 Salt bridges: B:R.98 GLY.7: 7 residues within 4Å: Chain A: R.98, L.150, S.162 Chain E: F.192, Y.235, T.237, F.240 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:T.237, A:S.162 Salt bridges: A:R.98 GLY.17: 7 residues within 4Å: Chain B: F.192, Y.235, T.237, F.240 Chain C: R.98, L.150, S.162 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.162, B:T.237 Salt bridges: C:R.98 GLY.27: 7 residues within 4Å: Chain C: F.192, Y.235, T.237, F.240 Chain D: R.98, L.150, S.162 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.162, C:T.237 Salt bridges: D:R.98 GLY.37: 7 residues within 4Å: Chain D: F.192, Y.235, T.237, F.240 Chain E: R.98, L.150, S.162 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.162, D:T.237 Salt bridges: E:R.98

25 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-functional Binders)(Non-covalent)

PIO.8: 1 residues within 4Å: Ligands: PIO.10 No protein-ligand interaction detected (PLIP) PIO.9: 2 residues within 4Å: Chain A: L.257 Ligands: PIO.50 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.257 PIO.10: 2 residues within 4Å: Chain A: W.448 Ligands: PIO.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.452 PIO.11: 1 residues within 4Å: Chain A: W.276 No protein-ligand interaction detected (PLIP) PIO.16: 3 residues within 4Å: Chain A: S.311, V.313 Ligands: PIO.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.313 PIO.18: 1 residues within 4Å: Ligands: PIO.20 No protein-ligand interaction detected (PLIP) PIO.19: 2 residues within 4Å: Chain B: L.257 Ligands: PIO.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.257 PIO.20: 2 residues within 4Å: Chain B: W.448 Ligands: PIO.18 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.452 PIO.21: 1 residues within 4Å: Chain B: W.276 No protein-ligand interaction detected (PLIP) PIO.26: 3 residues within 4Å: Chain B: S.311, V.313 Ligands: PIO.29 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.313 PIO.28: 1 residues within 4Å: Ligands: PIO.30 No protein-ligand interaction detected (PLIP) PIO.29: 2 residues within 4Å: Chain C: L.257 Ligands: PIO.26 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.257 PIO.30: 2 residues within 4Å: Chain C: W.448 Ligands: PIO.28 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.452 PIO.31: 1 residues within 4Å: Chain C: W.276 No protein-ligand interaction detected (PLIP) PIO.36: 3 residues within 4Å: Chain C: S.311, V.313 Ligands: PIO.39 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.313 PIO.38: 1 residues within 4Å: Ligands: PIO.40 No protein-ligand interaction detected (PLIP) PIO.39: 2 residues within 4Å: Chain D: L.257 Ligands: PIO.36 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.257 PIO.40: 2 residues within 4Å: Chain D: W.448 Ligands: PIO.38 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.452 PIO.41: 1 residues within 4Å: Chain D: W.276 No protein-ligand interaction detected (PLIP) PIO.46: 3 residues within 4Å: Chain D: S.311, V.313 Ligands: PIO.52 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.313 PIO.50: 3 residues within 4Å: Chain E: S.311, V.313 Ligands: PIO.9 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.313 PIO.51: 1 residues within 4Å: Ligands: PIO.53 No protein-ligand interaction detected (PLIP) PIO.52: 2 residues within 4Å: Chain E: L.257 Ligands: PIO.46 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.257 PIO.53: 2 residues within 4Å: Chain E: W.448 Ligands: PIO.51 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:K.452 PIO.54: 1 residues within 4Å: Chain E: W.276 No protein-ligand interaction detected (PLIP)

20 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PX4.12: 2 residues within 4Å: Chain A: W.276 Ligands: PX4.48 Ligand excluded by PLIP PX4.13: 3 residues within 4Å: Chain A: F.446, I.450, Y.451 Ligand excluded by PLIP PX4.14: 3 residues within 4Å: Chain A: S.329 Ligands: PX4.15, PX4.22 Ligand excluded by PLIP PX4.15: 3 residues within 4Å: Chain A: L.325, I.431 Ligands: PX4.14 Ligand excluded by PLIP PX4.22: 2 residues within 4Å: Chain B: W.276 Ligands: PX4.14 Ligand excluded by PLIP PX4.23: 3 residues within 4Å: Chain B: F.446, I.450, Y.451 Ligand excluded by PLIP PX4.24: 3 residues within 4Å: Chain B: S.329 Ligands: PX4.25, PX4.32 Ligand excluded by PLIP PX4.25: 3 residues within 4Å: Chain B: L.325, I.431 Ligands: PX4.24 Ligand excluded by PLIP PX4.32: 2 residues within 4Å: Chain C: W.276 Ligands: PX4.24 Ligand excluded by PLIP PX4.33: 3 residues within 4Å: Chain C: F.446, I.450, Y.451 Ligand excluded by PLIP PX4.34: 3 residues within 4Å: Chain C: S.329 Ligands: PX4.35, PX4.42 Ligand excluded by PLIP PX4.35: 3 residues within 4Å: Chain C: L.325, I.431 Ligands: PX4.34 Ligand excluded by PLIP PX4.42: 2 residues within 4Å: Chain D: W.276 Ligands: PX4.34 Ligand excluded by PLIP PX4.43: 3 residues within 4Å: Chain D: F.446, I.450, Y.451 Ligand excluded by PLIP PX4.44: 3 residues within 4Å: Chain D: S.329 Ligands: PX4.45, PX4.55 Ligand excluded by PLIP PX4.45: 3 residues within 4Å: Chain D: L.325, I.431 Ligands: PX4.44 Ligand excluded by PLIP PX4.47: 3 residues within 4Å: Chain E: F.446, I.450, Y.451 Ligand excluded by PLIP PX4.48: 3 residues within 4Å: Chain E: S.329 Ligands: PX4.12, PX4.49 Ligand excluded by PLIP PX4.49: 3 residues within 4Å: Chain E: L.325, I.431 Ligands: PX4.48 Ligand excluded by PLIP PX4.55: 2 residues within 4Å: Chain E: W.276 Ligands: PX4.44 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kindig, K. et al., Homomeric alpha3 glycine receptor in the presence of 1 mM glycine at pH 6.4 in a desensitized state. To Be Published

Release Date

2024-11-13

Peptides

Glycine receptor subunit alpha-3: 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 alpha-3

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