SMTL ID : 8dn4.1

Cryo-EM structure of human Glycine Receptor alpha-1 beta heteromer, glycine-bound state3(desensitized state)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: P.35, P.36, N.38, E.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.38 NAG.6: 3 residues within 4Å: Chain B: P.36, N.38, I.167 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.38 NAG.11: 3 residues within 4Å: Chain C: P.36, N.38, E.169 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.36, C:E.169 NAG.14: 3 residues within 4Å: Chain D: P.35, P.36, N.38 No protein-ligand interaction detected (PLIP) NAG.19: 3 residues within 4Å: Chain E: I.190, G.217, N.218 No protein-ligand interaction detected (PLIP)

1 x LNK: PENTANE(Non-functional Binders)

LNK.2: 2 residues within 4Å: Chain A: I.225 Ligands: NBU.16 No protein-ligand interaction detected (PLIP)

9 x HEX: HEXANE(Non-covalent)(Non-functional Binders)

HEX.3: 3 residues within 4Å: Chain A: M.350, I.354 Ligands: HEX.4 No protein-ligand interaction detected (PLIP) HEX.4: 2 residues within 4Å: Chain A: W.353 Ligands: HEX.3 No protein-ligand interaction detected (PLIP) HEX.7: 5 residues within 4Å: Chain B: M.350, W.353, I.354, K.357 Ligands: HEX.8 No protein-ligand interaction detected (PLIP) HEX.8: 4 residues within 4Å: Chain B: M.220, L.224, W.353 Ligands: HEX.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.353 HEX.10: 3 residues within 4Å: Chain B: I.285, I.355, Y.356 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.285, B:Y.356 HEX.12: 4 residues within 4Å: Chain C: M.220, L.224, W.353, K.357 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.353 HEX.13: 2 residues within 4Å: Chain C: L.224, I.225 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.225 HEX.17: 1 residues within 4Å: Chain D: W.353 No protein-ligand interaction detected (PLIP) HEX.20: 3 residues within 4Å: Chain A: V.280 Chain E: M.247 Ligands: NBU.5 No protein-ligand interaction detected (PLIP)

3 x NBU: N-BUTANE(Non-functional Binders)(Non-covalent)

NBU.5: 2 residues within 4Å: Chain A: V.280 Ligands: HEX.20 No protein-ligand interaction detected (PLIP) NBU.16: 4 residues within 4Å: Chain D: V.280, I.285 Ligands: LNK.2, DD9.15 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.280, D:I.285 NBU.18: 2 residues within 4Å: Chain D: L.224, I.225 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.225

1 x OCT: N-OCTANE(Non-covalent)

OCT.9: 3 residues within 4Å: Chain B: I.225, I.229 Chain E: I.310 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.225

1 x DD9: nonane(Non-covalent)

DD9.15: 6 residues within 4Å: Chain D: V.280, I.285, F.348, F.351, Y.356 Ligands: NBU.16 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., Asymmetric gating of a human hetero-pentameric glycine receptor. Nat Commun (2023)

Release Date

2023-10-11

Peptides

Glycine receptor subunit alpha-1: ABCD
Glycine receptor subunit beta,Green fluorescent protein,Glycine receptor beta: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

E
E

Membrane

We predict this structure to be a membrane protein.
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Glycine receptor subunit alpha-1

Glycine receptor subunit beta,Green fluorescent protein,Glycine receptor beta

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