SMTL ID : 7w2g.1 (3 other biounits)

An open-like conformation of the sigma-1 receptor from Xenopus laevis complexed with PRE084 by soaking

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-trimer

Ligands

3 x E84: 2-morpholin-4-ylethyl 1-phenylcyclohexane-1-carboxylate(Non-covalent)

E84.1: 14 residues within 4Å: Chain A: V.85, W.90, M.94, Y.104, L.106, F.108, Y.121, I.125, D.127, W.165, E.173, T.182, F.185, Y.207 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.125, A:F.185, A:Y.207 Salt bridges: A:D.127, A:E.173 pi-Cation interactions: A:F.108 E84.2: 14 residues within 4Å: Chain B: V.85, W.90, Y.104, F.108, S.118, Y.121, I.125, D.127, W.165, E.173, T.182, F.185, A.186, Y.207 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.125, B:F.185, B:A.186, B:Y.207 Salt bridges: B:D.127, B:E.173 pi-Cation interactions: B:F.108 E84.4: 13 residues within 4Å: Chain C: V.85, W.90, Y.104, F.108, Y.121, I.125, D.127, W.165, E.173, T.182, F.185, A.186, Y.207 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.90, C:I.125, C:F.185, C:A.186, C:Y.207 Salt bridges: C:D.127, C:E.173 pi-Cation interactions: C:F.108

1 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.3: 7 residues within 4Å: Chain A: S.167, G.168 Chain B: T.133, R.135, S.144, I.146, Q.164 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.135, B:I.146 Hydrogen bonds: B:R.135, B:S.144, A:S.167, A:S.167 Salt bridges: B:R.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meng, F. et al., An open-like conformation of the sigma-1 receptor reveals its ligand entry pathway. Nat Commun (2022)

Release Date

2022-03-16

Peptides

Sigma non-opioid intracellular receptor 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Sigma non-opioid intracellular receptor 1

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