SMTL ID : 7m95.1

Bovine sigma-2 receptor bound to Z1241145220

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

2 x ZNC: 3-[1-(3-phenylpropyl)-1,2,3,6-tetrahydropyridin-4-yl]-1H-pyrrolo[2,3-b]pyridine(Non-covalent)

ZNC.1: 11 residues within 4Å: Chain A: H.27, M.34, D.35, Y.56, F.75, E.79, Q.83, T.116, V.152, Y.153, Y.156 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.56, A:Y.56, A:T.116, A:Y.153, A:Y.156 Hydrogen bonds: A:Q.83, A:Q.83 Salt bridges: A:D.35 ZNC.9: 13 residues within 4Å: Chain B: H.27, M.34, D.35, Y.56, L.65, F.75, L.76, E.79, Q.83, T.116, V.152, Y.153, Y.156 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.56, B:Y.56, B:L.76, B:V.152, B:Y.153, B:Y.156 Hydrogen bonds: B:Q.83, B:Q.83 Salt bridges: B:D.35

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 11 residues within 4Å: Chain A: L.32, L.33, L.44, Y.45, P.46, L.49, L.80, V.81, L.84, P.85 Ligands: OLC.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.32, A:L.32, A:L.33, A:L.44, A:Y.45, A:L.49, A:L.80, A:L.80, A:L.84, A:P.85 Hydrogen bonds: A:V.81

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

OLC.3: 2 residues within 4Å: Chain A: P.85 Ligands: OLC.5 No protein-ligand interaction detected (PLIP) OLC.4: 8 residues within 4Å: Chain A: F.82, F.86, P.105, I.108, Y.109, H.112 Chain B: T.115 Ligands: OLC.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.82, A:F.86, A:P.105, A:I.108, A:Y.109 OLC.5: 7 residues within 4Å: Chain A: F.82, P.85, F.86, I.89, W.101 Ligands: OLC.3, OLC.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.85, A:F.86, A:F.86, A:I.89, A:W.101 OLC.6: 5 residues within 4Å: Chain A: R.14, W.18, L.25, F.95 Ligands: OLC.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.18, A:W.18, A:L.25, A:F.95, A:F.95 OLC.7: 4 residues within 4Å: Chain A: L.25, Y.92, F.95 Ligands: OLC.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.25, A:Y.92, A:F.95 OLC.8: 5 residues within 4Å: Chain A: L.40, P.41, D.43, L.44 Ligands: CLR.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.40, A:P.41, A:D.43, A:L.44 OLC.10: 4 residues within 4Å: Chain B: W.18, L.25, F.95, K.96 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.18, B:L.25, B:K.96 OLC.11: 8 residues within 4Å: Chain A: M.114, I.118 Chain B: F.82, F.86, P.105, I.108, Y.109, H.112 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.82, B:F.82, B:F.86, B:P.105, A:I.118 OLC.12: 6 residues within 4Å: Chain B: L.32, L.33, L.44, P.46, L.80, L.84 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.33, B:L.80, B:L.84

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
A

B
B

Membrane

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

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