SMTL ID : 9j8d.1

Human Glycine Transporter 1 in the Iclepertin-Bound State with an Inward-Facing Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

monomer

Ligands

1 x 01: Iclepertin

01.1: 17 residues within 4Å: Chain A: Y.62, G.65, L.66, G.67, N.68, L.104, Y.142, Y.316, S.317, G.319, W.322, G.324, L.325, I.345, T.418, C.421 Ligands: NA.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.62, A:Y.62, A:W.322, A:W.322 pi-Stacking: A:Y.62

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: N.68, Y.88, Q.313, S.317, N.349, S.353 Ligand excluded by PLIP

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 9 residues within 4Å: Chain A: V.484, C.487, I.488, V.491, Y.495, R.523, P.527, F.531, L.534 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.484, A:I.488, A:V.491, A:Y.495, A:Y.495, A:P.527, A:F.531 CLR.4: 6 residues within 4Å: Chain A: N.475, Y.476, S.479, F.480, F.560, V.567 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.476, A:F.480, A:F.560, A:V.567 CLR.5: 6 residues within 4Å: Chain A: L.234, G.238, G.241, F.248, A.451, F.455 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.248, A:A.451, A:F.455

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: V.64, L.414, T.418 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.418 NA.7: 4 residues within 4Å: Chain A: Y.62, S.317, L.318 Ligands: 01.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.317

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, N. et al., Modulation of the human GlyT1 by clinical drugs and cholesterol. Nat Commun (2025)

Release Date

2025-03-05

Peptides

Isoform GlyT-1B of Sodium- and chloride-dependent glycine transporter 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Isoform GlyT-1B of Sodium- and chloride-dependent glycine transporter 1

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