SMTL ID : 7tu9.1

Alpha1/BetaB Heteromeric Glycine Receptor in Strychnine-Bound State

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: N.55, P.59, P.60, N.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.60 NAG.6: 3 residues within 4Å: Chain B: P.59, P.60, N.62 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.59 Hydrogen bonds: B:P.60 NAG.14: 5 residues within 4Å: Chain C: P.59, P.60, N.62, I.191, E.193 No protein-ligand interaction detected (PLIP) NAG.21: 4 residues within 4Å: Chain D: N.55, P.59, P.60, N.62 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.55, D:N.62 NAG.27: 2 residues within 4Å: Chain E: N.135, D.202 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.202 NAG.28: 3 residues within 4Å: Chain E: M.294, N.322, T.324 No protein-ligand interaction detected (PLIP)

10 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.2: 1 residues within 4Å: Chain A: P.419 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.419 PIO.5: 4 residues within 4Å: Chain A: S.320, E.324, A.327 Ligands: PX4.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.324, A:A.327 PIO.10: 2 residues within 4Å: Ligands: PX4.13, PIO.17 No protein-ligand interaction detected (PLIP) PIO.11: 4 residues within 4Å: Chain B: L.323, E.324, I.410 Ligands: PX4.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.323, B:E.324 PIO.12: 2 residues within 4Å: Chain B: P.419, L.420 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.419, B:L.420 PIO.17: 3 residues within 4Å: Chain C: W.267, V.416 Ligands: PIO.10 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.267 PIO.22: 2 residues within 4Å: Chain D: L.323, F.330 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.323, D:F.330 PIO.29: 2 residues within 4Å: Chain E: P.560, L.564 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:P.560, E:L.564 PIO.30: 4 residues within 4Å: Chain B: I.260, W.267 Chain E: V.429, V.432 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.429 PIO.31: 3 residues within 4Å: Chain E: R.550, I.551, Y.554 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:I.551, E:Y.554 Salt bridges: E:R.550

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

PX4.3: 6 residues within 4Å: Chain A: L.316, R.409, I.410, V.413, S.414, F.418 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.316, A:I.410, A:V.413 Salt bridges: A:R.409 PX4.8: 6 residues within 4Å: Chain B: L.316, R.409, I.410, V.413, F.418 Ligands: PIO.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.316, B:I.410, B:F.418 Salt bridges: B:R.409 PX4.9: 1 residues within 4Å: Chain B: V.416 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.416 PX4.13: 4 residues within 4Å: Chain B: A.326, F.330 Chain C: W.267 Ligands: PIO.10 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:A.326, C:W.267, C:W.267, C:W.267 PX4.16: 5 residues within 4Å: Chain C: S.320, I.410, A.417, F.418, V.421 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.410, C:A.417, C:V.421 PX4.20: 4 residues within 4Å: Chain C: A.326, F.330 Chain D: V.264, W.267 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.264, D:W.267, D:W.267, C:F.330 PX4.23: 5 residues within 4Å: Chain D: S.320, V.413, S.414, A.417, V.421 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.413, D:A.417, D:V.421 PX4.24: 2 residues within 4Å: Chain D: W.267, V.416 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.267, D:V.416 PX4.25: 7 residues within 4Å: Chain A: A.326, A.327, F.330 Chain E: L.366, W.369 Ligands: PIO.5, PX4.26 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:A.326, A:F.330, E:L.366, E:W.369, E:W.369 PX4.26: 1 residues within 4Å: Ligands: PX4.25 No protein-ligand interaction detected (PLIP)

5 x SY9: STRYCHNINE(Non-covalent)

SY9.4: 9 residues within 4Å: Chain A: F.183, Y.226, T.228, F.231 Chain E: F.187, R.189, L.242, F.244, S.254 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:Y.226, A:Y.226, A:T.228, A:F.231, E:F.187, E:F.244 Hydrogen bonds: E:R.189 SY9.7: 9 residues within 4Å: Chain B: F.87, R.89, L.141, R.143, L.151, S.153 Chain E: F.284, Y.327, Y.333 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain B Hydrophobic interactions: E:Y.327, E:Y.333, B:L.141, B:L.141, B:L.151 Hydrogen bonds: B:R.89 SY9.15: 7 residues within 4Å: Chain B: F.183, Y.226, F.231 Chain C: F.87, R.89, L.141, R.143 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.183, B:Y.226, B:F.231, C:F.87, C:L.141, C:L.141 Hydrogen bonds: C:R.89 SY9.18: 9 residues within 4Å: Chain A: F.87, R.89, L.141, R.143, S.153 Chain D: F.183, Y.226, T.228, F.231 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Y.226, D:T.228, D:F.231, A:L.141 Hydrogen bonds: A:R.89 SY9.19: 9 residues within 4Å: Chain C: F.183, G.184, Y.226, T.228, F.231 Chain D: F.87, R.89, L.141, R.143 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Y.226, C:T.228, C:F.231, C:F.231, D:F.87, D:L.141, D:L.141 Hydrogen bonds: D:R.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gibbs, E. et al., Conformational transitions and allosteric modulation in a heteromeric glycine receptor. Nat Commun (2023)

Release Date

2023-03-22

Peptides

Glycine receptor subunit alphaZ1: ABCD
Glycine receptor beta subunit 2: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
C

D
B

E
E

Membrane

We predict this structure to be a membrane protein.
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Glycine receptor subunit alphaZ1

Glycine receptor beta subunit 2

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