SMTL ID : 7l31.1

Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, strychnine bound state, 3.8 Angstrom

Coordinates

PDB Format Compare

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: 4 residues within 4Å: Chain A: P.42, P.43, N.45, E.176 No protein-ligand interaction detected (PLIP) NAG.2: 2 residues within 4Å: Chain A: T.47, N.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.76 NAG.4: 4 residues within 4Å: Chain B: N.38, 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: 4 residues within 4Å: Chain B: N.45, T.47, N.76 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.47 NAG.7: 5 residues within 4Å: Chain C: P.43, V.44, N.45, I.174 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.45 NAG.8: 4 residues within 4Å: Chain C: N.45, T.47, N.76 Ligands: NAG.7 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.45, C:T.47 Hydrogen bonds: C:N.76 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, T.47, N.76 No protein-ligand interaction detected (PLIP) NAG.14: 4 residues within 4Å: Chain E: R.210, F.211, I.212, N.240 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:I.212, E:N.240 Hydrogen bonds: E:R.210

5 x SY9: STRYCHNINE(Non-covalent)

SY9.3: 10 residues within 4Å: Chain A: F.70, R.72, L.124, R.126, L.134, S.136 Chain E: F.202, G.203, Y.245, Y.251 11 PLIP interactions: 5 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: E:F.202, E:Y.245, E:Y.245, E:Y.251, E:Y.251, A:F.70, A:R.72, A:L.124, A:L.124, A:L.134 Hydrogen bonds: A:R.72 SY9.6: 10 residues within 4Å: Chain A: F.166, G.167, Y.209, T.211, F.214 Chain B: F.70, R.72, L.124, R.126, S.136 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.70, B:L.124, A:Y.209, A:Y.209, A:T.211, A:F.214, A:F.214 SY9.9: 10 residues within 4Å: Chain B: F.166, Y.209, F.214 Chain C: F.51, F.70, R.72, L.124, R.126, L.134, S.136 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.209, B:Y.209, B:Y.209, B:F.214, C:F.70, C:R.72, C:L.124, C:L.134 Salt bridges: B:E.164 SY9.12: 10 residues within 4Å: Chain C: F.166, Y.209, T.211, F.214 Chain D: F.70, R.72, L.124, R.126, L.134, S.136 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:F.70, D:R.72, D:L.124, D:L.134, C:Y.209, C:Y.209, C:T.211, C:F.214, C:F.214 SY9.13: 10 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, S.172 8 PLIP interactions: 5 interactions with chain D, 3 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:L.160, E:F.162

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: 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

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