SMTL ID : 7w2b.1 (3 other biounits)

The closed conformation of the sigma-1 receptor from Xenopus laevis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-trimer

Ligands

6 x AU: GOLD ION(Non-covalent)

AU.1: 5 residues within 4Å: Chain A: L.80, Q.81, W.82, C.95 Ligands: AU.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.95 AU.2: 5 residues within 4Å: Chain A: I.63, W.82, C.95, L.107 Ligands: AU.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.95 AU.4: 5 residues within 4Å: Chain B: L.80, Q.81, W.82, C.95 Ligands: AU.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.95 AU.5: 4 residues within 4Å: Chain B: W.82, C.95, L.107 Ligands: AU.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.95 AU.7: 5 residues within 4Å: Chain C: L.80, Q.81, W.82, C.95 Ligands: AU.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.95 AU.8: 5 residues within 4Å: Chain C: I.63, W.82, C.95, L.107 Ligands: AU.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.95

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

BOG.3: 7 residues within 4Å: Chain A: T.133, R.135, S.144, I.146, Q.164 Chain C: S.167, G.168 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:R.135, A:I.146, A:Q.164 Hydrogen bonds: A:R.135, A:S.144, C:S.167 Salt bridges: A:R.135 BOG.6: 7 residues within 4Å: Chain A: S.167, G.168 Chain B: T.133, R.135, S.144, I.146, Q.164 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.135, B:I.146 Hydrogen bonds: B:R.135, B:S.144, A:S.167 Salt bridges: B:R.135 BOG.9: 7 residues within 4Å: Chain B: S.167, G.168 Chain C: T.133, R.135, S.144, I.146, Q.164 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:R.135 Hydrogen bonds: C:R.135, C:S.144, B:S.167 Salt bridges: C: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
C

C
E

Membrane

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

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