SMTL ID : 9bwg.1

Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine and 0.1 mM zinc 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.162 Salt bridges: B:R.98 GLY.9: 8 residues within 4Å: Chain A: F.96, R.98, L.150, S.162 Chain E: F.192, Y.235, T.237, F.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.162 Salt bridges: A:R.98 GLY.19: 8 residues within 4Å: Chain B: F.192, Y.235, T.237, F.240 Chain C: F.96, R.98, L.150, S.162 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.162 Salt bridges: C:R.98 GLY.31: 7 residues within 4Å: Chain C: F.192, Y.235, T.237, F.240 Chain D: R.98, L.150, S.162 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.162 Salt bridges: D:R.98 GLY.43: 8 residues within 4Å: Chain D: F.192, Y.235, T.237, F.240 Chain E: F.96, R.98, L.150, S.162 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.162 Salt bridges: E:R.98

10 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: E.225, D.227, H.248, I.459, H.460 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.225, A:D.227, A:D.227, A:H.248, A:H.460 ZN.8: 5 residues within 4Å: Chain A: E.136, A.139 Chain B: H.142, E.143, V.144 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.142, A:E.136, A:E.136, H2O.1 ZN.20: 5 residues within 4Å: Chain B: E.225, D.227, H.248, I.459, H.460 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.225, B:D.227, B:D.227, B:H.248, B:H.460 ZN.21: 4 residues within 4Å: Chain B: E.136, A.139 Chain C: H.142, V.144 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.136, B:E.136, C:H.142, H2O.1 ZN.32: 5 residues within 4Å: Chain C: E.225, D.227, H.248, I.459, H.460 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.225, C:D.227, C:D.227, C:H.248, C:H.460 ZN.33: 5 residues within 4Å: Chain C: E.136, A.139 Chain D: H.142, E.143, V.144 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:H.142, C:E.136, C:E.136, H2O.1 ZN.44: 5 residues within 4Å: Chain D: E.225, D.227, H.248, I.459, H.460 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.225, D:D.227, D:D.227, D:H.248, D:H.460 ZN.45: 4 residues within 4Å: Chain D: E.136, A.139 Chain E: H.142, V.144 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:H.142, D:E.136, D:E.136, H2O.1 ZN.55: 5 residues within 4Å: Chain E: E.225, D.227, H.248, I.459, H.460 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.225, E:D.227, E:D.227, E:H.248, E:H.460 ZN.56: 4 residues within 4Å: Chain A: H.142, V.144 Chain E: E.136, A.139 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: E:E.136, E:E.136, A:H.142, H2O.1

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.10: 1 residues within 4Å: Ligands: PIO.12 No protein-ligand interaction detected (PLIP) PIO.11: 2 residues within 4Å: Ligands: PIO.12, PIO.60 No protein-ligand interaction detected (PLIP) PIO.12: 5 residues within 4Å: Chain A: L.257, W.448, K.452 Ligands: PIO.10, PIO.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.257, A:W.448, A:W.448 Salt bridges: A:K.452 PIO.13: 1 residues within 4Å: Chain A: W.276 No protein-ligand interaction detected (PLIP) PIO.18: 5 residues within 4Å: Chain A: S.311, V.313 Chain B: I.258, I.262 Ligands: PIO.23 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.313, B:I.258, B:I.262 PIO.22: 1 residues within 4Å: Ligands: PIO.24 No protein-ligand interaction detected (PLIP) PIO.23: 2 residues within 4Å: Ligands: PIO.18, PIO.24 No protein-ligand interaction detected (PLIP) PIO.24: 5 residues within 4Å: Chain B: L.257, W.448, K.452 Ligands: PIO.22, PIO.23 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.257, B:W.448, B:W.448 Salt bridges: B:K.452 PIO.25: 1 residues within 4Å: Chain B: W.276 No protein-ligand interaction detected (PLIP) PIO.30: 5 residues within 4Å: Chain B: S.311, V.313 Chain C: I.258, I.262 Ligands: PIO.35 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.258, C:I.262, B:V.313 PIO.34: 1 residues within 4Å: Ligands: PIO.36 No protein-ligand interaction detected (PLIP) PIO.35: 2 residues within 4Å: Ligands: PIO.30, PIO.36 No protein-ligand interaction detected (PLIP) PIO.36: 5 residues within 4Å: Chain C: L.257, W.448, K.452 Ligands: PIO.34, PIO.35 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.257, C:W.448, C:W.448 Salt bridges: C:K.452 PIO.37: 1 residues within 4Å: Chain C: W.276 No protein-ligand interaction detected (PLIP) PIO.42: 5 residues within 4Å: Chain C: S.311, V.313 Chain D: I.258, I.262 Ligands: PIO.47 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.313, D:I.258, D:I.262 PIO.46: 1 residues within 4Å: Ligands: PIO.48 No protein-ligand interaction detected (PLIP) PIO.47: 2 residues within 4Å: Ligands: PIO.42, PIO.48 No protein-ligand interaction detected (PLIP) PIO.48: 5 residues within 4Å: Chain D: L.257, W.448, K.452 Ligands: PIO.46, PIO.47 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.257, D:W.448, D:W.448 Salt bridges: D:K.452 PIO.49: 1 residues within 4Å: Chain D: W.276 No protein-ligand interaction detected (PLIP) PIO.54: 5 residues within 4Å: Chain D: S.311, V.313 Chain E: I.258, I.262 Ligands: PIO.62 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:I.258, E:I.262, D:V.313 PIO.60: 5 residues within 4Å: Chain A: I.258, I.262 Chain E: S.311, V.313 Ligands: PIO.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:I.258, A:I.262, E:V.313 PIO.61: 1 residues within 4Å: Ligands: PIO.63 No protein-ligand interaction detected (PLIP) PIO.62: 2 residues within 4Å: Ligands: PIO.54, PIO.63 No protein-ligand interaction detected (PLIP) PIO.63: 5 residues within 4Å: Chain E: L.257, W.448, K.452 Ligands: PIO.61, PIO.62 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.257, E:W.448, E:W.448 Salt bridges: E:K.452 PIO.64: 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)

PX4.14: 5 residues within 4Å: Chain A: W.276 Chain E: L.332, V.340, Q.343 Ligands: PX4.57 Ligand excluded by PLIP PX4.15: 2 residues within 4Å: Chain A: S.329 Ligands: PX4.26 Ligand excluded by PLIP PX4.16: 4 residues within 4Å: Chain A: L.325, F.326, I.431, C.435 Ligand excluded by PLIP PX4.17: 5 residues within 4Å: Chain A: I.318, I.442, F.446, I.450, Y.451 Ligand excluded by PLIP PX4.26: 5 residues within 4Å: Chain A: L.332, V.340, Q.343 Chain B: W.276 Ligands: PX4.15 Ligand excluded by PLIP PX4.27: 3 residues within 4Å: Chain B: S.329, L.332 Ligands: PX4.38 Ligand excluded by PLIP PX4.28: 4 residues within 4Å: Chain B: L.325, F.326, I.431, C.435 Ligand excluded by PLIP PX4.29: 5 residues within 4Å: Chain B: I.318, I.442, F.446, I.450, Y.451 Ligand excluded by PLIP PX4.38: 6 residues within 4Å: Chain B: L.332, F.339, V.340, Q.343 Chain C: W.276 Ligands: PX4.27 Ligand excluded by PLIP PX4.39: 2 residues within 4Å: Chain C: S.329 Ligands: PX4.50 Ligand excluded by PLIP PX4.40: 4 residues within 4Å: Chain C: L.325, F.326, I.431, C.435 Ligand excluded by PLIP PX4.41: 5 residues within 4Å: Chain C: I.318, I.442, F.446, I.450, Y.451 Ligand excluded by PLIP PX4.50: 5 residues within 4Å: Chain C: L.332, V.340, Q.343 Chain D: W.276 Ligands: PX4.39 Ligand excluded by PLIP PX4.51: 3 residues within 4Å: Chain D: S.329, L.332 Ligands: PX4.65 Ligand excluded by PLIP PX4.52: 4 residues within 4Å: Chain D: L.325, F.326, I.431, C.435 Ligand excluded by PLIP PX4.53: 5 residues within 4Å: Chain D: I.318, I.442, F.446, I.450, Y.451 Ligand excluded by PLIP PX4.57: 2 residues within 4Å: Chain E: S.329 Ligands: PX4.14 Ligand excluded by PLIP PX4.58: 4 residues within 4Å: Chain E: L.325, F.326, I.431, C.435 Ligand excluded by PLIP PX4.59: 5 residues within 4Å: Chain E: I.318, I.442, F.446, I.450, Y.451 Ligand excluded by PLIP PX4.65: 6 residues within 4Å: Chain D: L.332, F.339, V.340, Q.343 Chain E: W.276 Ligands: PX4.51 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kindig, K. et al., Physiological modulation of alpha3 glycine receptors. 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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