SMTL ID : 7m96.2 (1 other biounit)

Bovine sigma-2 receptor bound to Z4857158944

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

2 x YTD: 6-({[(1S)-1-hydroxy-2-methyl-1-phenylpropan-2-yl]amino}methyl)-1-methyl-3,4-dihydroquinolin-2(1H)-one(Non-covalent)

YTD.1: 11 residues within 4Å: Chain A: H.27, I.30, D.35, F.72, F.75, E.79, Q.83, T.116, V.152, Y.153, Y.156 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.30, A:F.72, A:V.152, A:Y.153, A:Y.156, A:Y.156 Hydrogen bonds: A:Q.83 YTD.5: 15 residues within 4Å: Chain B: H.27, I.30, M.34, D.35, Y.56, L.65, F.72, F.75, E.79, Q.83, T.113, T.116, V.152, Y.153, Y.156 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.30, B:M.34, B:Y.56, B:L.65, B:F.72, B:F.72, B:T.113, B:Y.153, B:Y.153 Hydrogen bonds: B:D.35, B:Q.83, B:Y.156

8 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 4 residues within 4Å: Chain A: F.86, I.89, W.101 Ligands: OLC.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.86, A:I.89, A:I.89, A:W.101 OLC.3: 6 residues within 4Å: Chain A: F.82, P.105, Y.109, H.112 Chain B: M.114 Ligands: OLC.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.82, A:P.105, A:Y.109, A:H.112 OLC.4: 4 residues within 4Å: Chain A: S.74, F.77 Chain B: S.122, L.126 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.126, A:F.77, A:F.77, A:F.77 OLC.6: 7 residues within 4Å: Chain A: M.114 Chain B: F.82, F.86, P.105, I.108, H.112 Ligands: OLC.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.82, B:F.86, B:P.105, B:I.108, B:H.112 OLC.7: 5 residues within 4Å: Chain B: L.25, I.28, P.88, Y.92, K.96 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.25, B:I.28, B:P.88, B:Y.92, B:Y.92, B:K.96, B:K.96 OLC.8: 3 residues within 4Å: Chain B: W.101, P.105 Ligands: OLC.6 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.101 OLC.9: 3 residues within 4Å: Chain B: I.162, L.165, F.166 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.162, B:L.165, B:F.166, B:F.166 OLC.10: 2 residues within 4Å: Chain B: W.18, F.22 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.18, B:F.22

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.11: 2 residues within 4Å: Chain B: P.41, R.42 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alon, A. et al., Structures of the sigma 2 receptor enable docking for bioactive ligand discovery. Nature (2021)

Release Date

2021-12-15

Peptides

Sigma intracellular receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Membrane

We predict this structure to be a membrane protein.
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Sigma intracellular receptor 2

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