SMTL ID : 5bkf.1

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

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: 3 residues within 4Å: Chain A: N.38, P.43, N.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.38, A:P.43 NAG.2: 3 residues within 4Å: Chain A: N.45, N.76, N.130 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.76 NAG.4: 2 residues within 4Å: Chain B: P.43, N.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.43 NAG.5: 2 residues within 4Å: Chain B: N.45, N.76 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.45, B:N.76 NAG.7: 4 residues within 4Å: Chain C: P.42, P.43, N.45, I.174 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain C: N.45, W.75, N.76, N.130 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.76 Hydrogen bonds: C:N.130 NAG.10: 3 residues within 4Å: Chain D: N.38, P.43, N.45 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.38, D:P.43, D:N.45 NAG.11: 3 residues within 4Å: Chain D: N.45, N.76, N.130 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.45, D:N.76 NAG.13: 3 residues within 4Å: Chain E: I.212, N.240, T.242 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.212 Hydrogen bonds: E:N.240

5 x GLY: GLYCINE(Non-covalent)

GLY.3: 8 residues within 4Å: Chain A: F.70, R.72, L.124, S.136 Chain E: F.202, Y.245, T.248, Y.251 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:S.136, E:F.202, E:T.248, E:T.248 Salt bridges: A:R.72 GLY.6: 8 residues within 4Å: Chain A: F.166, Y.209, T.211, F.214 Chain B: F.70, R.72, L.124, S.136 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.166, A:T.211, A:T.211, B:S.136 Salt bridges: B:R.72 GLY.9: 6 residues within 4Å: Chain B: F.166, T.211, F.214 Chain C: F.70, R.72, S.136 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.136, B:T.211, B:T.211 Salt bridges: C:R.72 GLY.12: 8 residues within 4Å: Chain C: F.166, Y.209, N.210, T.211, F.214 Chain D: F.70, R.72, S.136 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.136, C:T.211, C:T.211 Salt bridges: D:R.72 GLY.14: 7 residues within 4Å: Chain D: F.166, Y.209, T.211, F.214 Chain E: F.104, R.106, S.172 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:F.166, D:T.211, D:T.211, E:S.172 Salt bridges: 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: 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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