SMTL ID : 9bwj.1

Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine and 0.1 mM zinc in an apo 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)

10 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: E.225, D.227, H.248, 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.7: 2 residues within 4Å: Chain A: H.142 Chain E: E.136 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: A:H.142, E:E.136, E:E.136, H2O.1 ZN.15: 2 residues within 4Å: Chain A: E.136 Chain B: H.142 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.136, A:E.136, B:H.142, H2O.1 ZN.16: 4 residues within 4Å: Chain B: E.225, D.227, H.248, 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.24: 2 residues within 4Å: Chain B: E.136 Chain C: H.142 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.25: 4 residues within 4Å: Chain C: E.225, D.227, H.248, 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: 2 residues within 4Å: Chain C: E.136 Chain D: H.142 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.34: 4 residues within 4Å: Chain D: E.225, D.227, H.248, 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.42: 2 residues within 4Å: Chain D: E.136 Chain E: H.142 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.43: 4 residues within 4Å: Chain E: E.225, D.227, H.248, 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

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

PX4.8: 1 residues within 4Å: Chain A: I.453 Ligand excluded by PLIP PX4.9: 2 residues within 4Å: Chain A: W.448, K.452 Ligand excluded by PLIP PX4.10: 2 residues within 4Å: Chain A: I.318, V.322 Ligand excluded by PLIP PX4.11: 3 residues within 4Å: Chain A: F.446, Y.451, R.455 Ligand excluded by PLIP PX4.12: 7 residues within 4Å: Chain A: L.325, F.326, S.329, K.427, I.428, F.436 Ligands: PX4.13 Ligand excluded by PLIP PX4.13: 3 residues within 4Å: Chain A: S.329, A.336 Ligands: PX4.12 Ligand excluded by PLIP PX4.14: 4 residues within 4Å: Chain A: L.332, F.339 Chain B: V.273, W.276 Ligand excluded by PLIP PX4.17: 1 residues within 4Å: Chain B: I.453 Ligand excluded by PLIP PX4.18: 2 residues within 4Å: Chain B: W.448, K.452 Ligand excluded by PLIP PX4.19: 2 residues within 4Å: Chain B: I.318, V.322 Ligand excluded by PLIP PX4.20: 3 residues within 4Å: Chain B: F.446, Y.451, R.455 Ligand excluded by PLIP PX4.21: 7 residues within 4Å: Chain B: L.325, F.326, S.329, K.427, I.428, F.436 Ligands: PX4.22 Ligand excluded by PLIP PX4.22: 3 residues within 4Å: Chain B: S.329, A.336 Ligands: PX4.21 Ligand excluded by PLIP PX4.23: 4 residues within 4Å: Chain B: L.332, F.339 Chain C: V.273, W.276 Ligand excluded by PLIP PX4.26: 1 residues within 4Å: Chain C: I.453 Ligand excluded by PLIP PX4.27: 2 residues within 4Å: Chain C: W.448, K.452 Ligand excluded by PLIP PX4.28: 2 residues within 4Å: Chain C: I.318, V.322 Ligand excluded by PLIP PX4.29: 3 residues within 4Å: Chain C: F.446, Y.451, R.455 Ligand excluded by PLIP PX4.30: 7 residues within 4Å: Chain C: L.325, F.326, S.329, K.427, I.428, F.436 Ligands: PX4.31 Ligand excluded by PLIP PX4.31: 3 residues within 4Å: Chain C: S.329, A.336 Ligands: PX4.30 Ligand excluded by PLIP PX4.32: 4 residues within 4Å: Chain C: L.332, F.339 Chain D: V.273, W.276 Ligand excluded by PLIP PX4.35: 1 residues within 4Å: Chain D: I.453 Ligand excluded by PLIP PX4.36: 2 residues within 4Å: Chain D: W.448, K.452 Ligand excluded by PLIP PX4.37: 2 residues within 4Å: Chain D: I.318, V.322 Ligand excluded by PLIP PX4.38: 3 residues within 4Å: Chain D: F.446, Y.451, R.455 Ligand excluded by PLIP PX4.39: 7 residues within 4Å: Chain D: L.325, F.326, S.329, K.427, I.428, F.436 Ligands: PX4.40 Ligand excluded by PLIP PX4.40: 3 residues within 4Å: Chain D: S.329, A.336 Ligands: PX4.39 Ligand excluded by PLIP PX4.41: 4 residues within 4Å: Chain D: L.332, F.339 Chain E: V.273, W.276 Ligand excluded by PLIP PX4.44: 2 residues within 4Å: Chain E: I.318, V.322 Ligand excluded by PLIP PX4.45: 3 residues within 4Å: Chain E: F.446, Y.451, R.455 Ligand excluded by PLIP PX4.46: 7 residues within 4Å: Chain E: L.325, F.326, S.329, K.427, I.428, F.436 Ligands: PX4.47 Ligand excluded by PLIP PX4.47: 3 residues within 4Å: Chain E: S.329, A.336 Ligands: PX4.46 Ligand excluded by PLIP PX4.48: 4 residues within 4Å: Chain A: V.273, W.276 Chain E: L.332, F.339 Ligand excluded by PLIP PX4.49: 1 residues within 4Å: Chain E: I.453 Ligand excluded by PLIP PX4.50: 2 residues within 4Å: Chain E: W.448, K.452 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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