SMTL ID : 7kuy.1

Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, strychnine bound state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: P.42, P.43, N.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.45 NAG.2: 2 residues within 4Å: Chain A: T.47, N.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.76, A:N.130 NAG.4: 5 residues within 4Å: Chain B: N.38, P.42, P.43, N.45 Ligands: NAG.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.43, B:N.45 NAG.5: 3 residues within 4Å: Chain B: N.76, K.132 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain C: N.38, P.42, P.43, N.45, I.174 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.42 Hydrogen bonds: C:N.38 NAG.8: 3 residues within 4Å: Chain C: T.47, N.76, K.132 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.47 NAG.10: 2 residues within 4Å: Chain D: P.43, N.45 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain D: N.45, N.76, K.132 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.45 Hydrogen bonds: D:K.132 NAG.13: 4 residues within 4Å: Chain E: R.210, I.212, N.240, T.242 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:R.210, E:I.212

5 x SY9: STRYCHNINE(Non-covalent)

SY9.3: 10 residues within 4Å: Chain A: F.51, F.70, R.72, L.124, L.134, S.136 Chain E: F.202, G.203, Y.245, Y.251 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: A:F.51, A:F.70, A:F.70, A:R.72, A:L.124, A:L.124, A:L.134, E:F.202, E:Y.245, E:Y.251, E:Y.251 SY9.6: 11 residues within 4Å: Chain A: E.164, F.166, G.167, Y.209, T.211, F.214 Chain B: F.70, R.72, L.124, R.126, L.134 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.70, B:L.124, A:F.166, A:Y.209, A:T.211, A:F.214, A:F.214 Salt bridges: A:E.164 SY9.9: 11 residues within 4Å: Chain B: F.166, G.167, Y.209, T.211, F.214 Chain C: F.70, R.72, L.124, R.126, L.134, S.136 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.166, B:Y.209, B:Y.209, B:Y.209, B:F.214, B:F.214, C:R.72, C:L.124, C:L.134 Salt bridges: B:E.164 SY9.12: 11 residues within 4Å: Chain C: E.164, F.166, Y.209, T.211, F.214 Chain D: F.51, F.70, R.72, L.124, L.134, S.136 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:F.70, D:L.124, D:L.134, C:F.166, C:Y.209, C:Y.209, C:F.214, C:F.214 Salt bridges: C:E.164 SY9.14: 11 residues within 4Å: Chain D: F.166, Y.209, T.211, F.214 Chain E: F.85, F.104, R.106, L.160, F.162, L.170, S.172 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:Y.209, D:Y.209, D:T.211, D:F.214, D:F.214, E:F.104, E:R.106, E:L.160, E:F.162, E:L.170 Hydrogen bonds: E:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., Characterization of the subunit composition and structure of adult human glycine receptors. Neuron (2021)

Release Date

2021-09-08

Peptides

Glycine receptor subunit alpha-2: ABCD
Glycine receptor subunit beta, Green fluorescent protein chimera: E

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-2

Glycine receptor subunit beta, Green fluorescent protein chimera

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