SMTL ID : 9bzp.1

Homomeric alpha3 glycine receptor in the presence of 0.1 millimolar glycine and 1 micromolar 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: 6 residues within 4Å: Chain A: F.192, T.237, F.240 Chain B: R.98, L.150, S.162 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.191, A:T.237, B:S.162 Salt bridges: B:R.98 GLY.17: 6 residues within 4Å: Chain B: F.192, T.237, F.240 Chain C: R.98, L.150, S.162 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.191, B:T.237, C:S.162 Salt bridges: C:R.98 GLY.29: 6 residues within 4Å: Chain C: F.192, T.237, F.240 Chain D: R.98, L.150, S.162 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.162, C:S.191, C:T.237 Salt bridges: D:R.98 GLY.39: 6 residues within 4Å: Chain D: F.192, T.237, F.240 Chain E: R.98, L.150, S.162 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:S.191, D:T.237, E:S.162 Salt bridges: E:R.98 GLY.51: 6 residues within 4Å: Chain A: R.98, L.150, S.162 Chain E: F.192, T.237, F.240 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.191, E:T.237, A:S.162 Salt bridges: A:R.98

5 x ZN: ZINC ION(Non-covalent)

ZN.7: 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.18: 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.30: 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.40: 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.52: 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

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-covalent)(Non-functional Binders)

PIO.8: 3 residues within 4Å: Chain A: I.445, W.448 Ligands: PIO.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.445, A:W.448 PIO.9: 2 residues within 4Å: Ligands: PIO.10, PIO.56 No protein-ligand interaction detected (PLIP) PIO.10: 4 residues within 4Å: Chain A: M.253, W.448 Ligands: PIO.8, PIO.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.448 Salt bridges: A:K.452 PIO.11: 3 residues within 4Å: Chain A: W.276, R.433 Ligands: PX4.12 No protein-ligand interaction detected (PLIP) PIO.16: 3 residues within 4Å: Chain A: S.311 Chain B: I.258 Ligands: PIO.20 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.258 PIO.19: 3 residues within 4Å: Chain B: I.445, W.448 Ligands: PIO.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.445, B:W.448 PIO.20: 2 residues within 4Å: Ligands: PIO.16, PIO.21 No protein-ligand interaction detected (PLIP) PIO.21: 4 residues within 4Å: Chain B: M.253, W.448 Ligands: PIO.19, PIO.20 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.448 Salt bridges: B:K.452 PIO.22: 3 residues within 4Å: Chain B: W.276, R.433 Ligands: PX4.23 No protein-ligand interaction detected (PLIP) PIO.27: 3 residues within 4Å: Chain B: S.311 Chain C: I.258 Ligands: PIO.32 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.258 PIO.31: 3 residues within 4Å: Chain C: I.445, W.448 Ligands: PIO.33 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.445, C:W.448 PIO.32: 2 residues within 4Å: Ligands: PIO.27, PIO.33 No protein-ligand interaction detected (PLIP) PIO.33: 4 residues within 4Å: Chain C: M.253, W.448 Ligands: PIO.31, PIO.32 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.448 Salt bridges: C:K.452 PIO.34: 3 residues within 4Å: Chain C: W.276, R.433 Ligands: PX4.28 No protein-ligand interaction detected (PLIP) PIO.38: 3 residues within 4Å: Chain C: S.311 Chain D: I.258 Ligands: PIO.42 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.258 PIO.41: 3 residues within 4Å: Chain D: I.445, W.448 Ligands: PIO.43 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.445, D:W.448 PIO.42: 2 residues within 4Å: Ligands: PIO.38, PIO.43 No protein-ligand interaction detected (PLIP) PIO.43: 4 residues within 4Å: Chain D: M.253, W.448 Ligands: PIO.41, PIO.42 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.448 Salt bridges: D:K.452 PIO.44: 3 residues within 4Å: Chain D: W.276, R.433 Ligands: PX4.45 No protein-ligand interaction detected (PLIP) PIO.49: 3 residues within 4Å: Chain D: S.311 Chain E: I.258 Ligands: PIO.58 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.258 PIO.56: 3 residues within 4Å: Chain A: I.258 Chain E: S.311 Ligands: PIO.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.258 PIO.57: 3 residues within 4Å: Chain E: I.445, W.448 Ligands: PIO.59 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.445, E:W.448 PIO.58: 2 residues within 4Å: Ligands: PIO.49, PIO.59 No protein-ligand interaction detected (PLIP) PIO.59: 4 residues within 4Å: Chain E: M.253, W.448 Ligands: PIO.57, PIO.58 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.448 Salt bridges: E:K.452 PIO.60: 3 residues within 4Å: Chain E: W.276, R.433 Ligands: PX4.50 No protein-ligand interaction detected (PLIP)

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

PX4.12: 7 residues within 4Å: Chain A: V.273, W.276 Chain E: L.332, F.339, V.340, R.424 Ligands: PIO.11 Ligand excluded by PLIP PX4.13: 2 residues within 4Å: Chain A: I.318, I.450 Ligand excluded by PLIP PX4.14: 2 residues within 4Å: Chain A: S.329 Ligands: PX4.15 Ligand excluded by PLIP PX4.15: 4 residues within 4Å: Chain A: L.325, I.428, C.435 Ligands: PX4.14 Ligand excluded by PLIP PX4.23: 7 residues within 4Å: Chain A: L.332, F.339, V.340, R.424 Chain B: V.273, W.276 Ligands: PIO.22 Ligand excluded by PLIP PX4.24: 2 residues within 4Å: Chain B: I.318, I.450 Ligand excluded by PLIP PX4.25: 2 residues within 4Å: Chain B: S.329 Ligands: PX4.26 Ligand excluded by PLIP PX4.26: 4 residues within 4Å: Chain B: L.325, I.428, C.435 Ligands: PX4.25 Ligand excluded by PLIP PX4.28: 6 residues within 4Å: Chain B: L.332, F.339, R.424 Chain C: V.273, W.276 Ligands: PIO.34 Ligand excluded by PLIP PX4.35: 2 residues within 4Å: Chain C: I.318, I.450 Ligand excluded by PLIP PX4.36: 2 residues within 4Å: Chain C: S.329 Ligands: PX4.37 Ligand excluded by PLIP PX4.37: 4 residues within 4Å: Chain C: L.325, I.428, C.435 Ligands: PX4.36 Ligand excluded by PLIP PX4.45: 7 residues within 4Å: Chain C: L.332, F.339, V.340, R.424 Chain D: V.273, W.276 Ligands: PIO.44 Ligand excluded by PLIP PX4.46: 2 residues within 4Å: Chain D: I.318, I.450 Ligand excluded by PLIP PX4.47: 2 residues within 4Å: Chain D: S.329 Ligands: PX4.48 Ligand excluded by PLIP PX4.48: 4 residues within 4Å: Chain D: L.325, I.428, C.435 Ligands: PX4.47 Ligand excluded by PLIP PX4.50: 7 residues within 4Å: Chain D: L.332, F.339, V.340, R.424 Chain E: V.273, W.276 Ligands: PIO.60 Ligand excluded by PLIP PX4.53: 2 residues within 4Å: Chain E: I.318, I.450 Ligand excluded by PLIP PX4.54: 2 residues within 4Å: Chain E: S.329 Ligands: PX4.55 Ligand excluded by PLIP PX4.55: 4 residues within 4Å: Chain E: L.325, I.428, C.435 Ligands: PX4.54 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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