SMTL ID : 6djz.1

Human sigma-1 receptor bound to haloperidol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.08 Å

Oligo State

homo-trimer

Ligands

3 x GMJ: 4-[4-(4-chlorophenyl)-4-hydroxypiperidin-1-yl]-1-(4-fluorophenyl)butan-1-one(Non-covalent)

GMJ.1: 19 residues within 4Å: Chain A: M.97, Y.107, L.109, S.121, Y.124, I.128, D.130, F.137, Q.139, V.156, V.157, H.158, T.164, V.166, E.176, T.185, L.186, A.189, Y.210 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.109, A:Y.124, A:I.128, A:H.158, A:V.166, A:L.186, A:A.189 Hydrogen bonds: A:Y.124 Salt bridges: A:D.130, A:E.176 pi-Stacking: A:Y.107, A:F.137 Halogen bonds: A:Q.139 GMJ.14: 18 residues within 4Å: Chain B: W.93, Y.107, L.109, S.121, Y.124, I.128, D.130, F.137, Q.139, V.156, H.158, T.164, V.166, W.168, E.176, T.185, L.186, A.189 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.107, B:L.109, B:Y.124, B:I.128, B:F.137, B:H.158, B:V.166, B:W.168, B:L.186, B:A.189 Hydrogen bonds: B:Y.124, B:Y.124 Salt bridges: B:D.130, B:E.176 pi-Cation interactions: B:H.158 Halogen bonds: B:Q.139 GMJ.20: 18 residues within 4Å: Chain C: W.93, M.97, L.99, A.102, L.109, S.121, Y.124, D.130, F.137, Q.139, V.156, H.158, V.166, E.176, T.185, L.186, A.189, Y.210 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.99, C:L.109, C:V.166, C:L.186, C:A.189 Hydrogen bonds: C:Y.124 Salt bridges: C:E.176 pi-Stacking: C:Y.107 Halogen bonds: C:Q.139

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: E.82, R.212, R.215 Ligands: OLC.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.82 Salt bridges: A:R.212, A:R.215 SO4.3: 4 residues within 4Å: Chain A: F.41, Q.42, R.43, R.179 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.42, A:R.43 Salt bridges: A:R.43, A:R.179 SO4.4: 5 residues within 4Å: Chain A: L.56, D.57, H.58, S.134, N.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.56, A:H.58, A:S.134 Salt bridges: A:H.58 SO4.5: 1 residues within 4Å: Chain A: R.208 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.208 SO4.6: 3 residues within 4Å: Chain A: R.118 Chain B: R.118 Chain C: R.118 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Salt bridges: C:R.118, B:R.118, A:R.118 SO4.7: 1 residues within 4Å: Chain A: R.64 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.64 SO4.8: 2 residues within 4Å: Chain A: R.141, T.144 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.141 SO4.15: 2 residues within 4Å: Chain B: R.212, R.215 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.212, B:R.215 SO4.16: 1 residues within 4Å: Chain B: R.208 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.208 SO4.17: 3 residues within 4Å: Chain B: Q.42, R.43, R.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.43 Salt bridges: B:R.179 SO4.18: 4 residues within 4Å: Chain B: L.56, D.57, H.58, S.134 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.58, B:S.134 Salt bridges: B:H.58 SO4.21: 4 residues within 4Å: Chain C: E.82, R.208, R.212, R.215 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.82 Salt bridges: C:R.212, C:R.215 SO4.22: 3 residues within 4Å: Chain C: Q.42, R.43, R.179 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.43 Salt bridges: C:R.179 SO4.23: 1 residues within 4Å: Chain C: R.208 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.208 SO4.24: 3 residues within 4Å: Chain C: D.57, H.58, S.134 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.56, C:H.58, C:S.134 Salt bridges: C:H.58

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: F.62, L.83, W.85, C.98 No protein-ligand interaction detected (PLIP) GOL.10: 4 residues within 4Å: Chain A: S.63, I.66, D.80, L.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.63, A:R.70, A:D.80 GOL.19: 2 residues within 4Å: Chain B: L.83, W.85 No protein-ligand interaction detected (PLIP) GOL.25: 4 residues within 4Å: Chain C: L.83, W.85, C.98 Ligands: GOL.26 No protein-ligand interaction detected (PLIP) GOL.26: 2 residues within 4Å: Chain C: D.80 Ligands: GOL.25 No protein-ligand interaction detected (PLIP)

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

OLC.11: 3 residues within 4Å: Chain A: W.33, L.104, Y.221 No protein-ligand interaction detected (PLIP) OLC.12: 2 residues within 4Å: Chain A: E.127, R.179 No protein-ligand interaction detected (PLIP) OLC.13: 5 residues within 4Å: Chain A: L.207, R.208, A.211, R.215 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.215 OLC.27: 4 residues within 4Å: Chain C: W.125, E.127, R.179, G.180 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.127 OLC.28: 6 residues within 4Å: Chain C: W.33, Q.37, L.104, S.105, G.180, V.181 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.37, C:G.180 OLC.29: 4 residues within 4Å: Chain C: W.33, Q.37, S.105 Ligands: OLC.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.105, C:S.105 OLC.30: 6 residues within 4Å: Chain C: S.103, L.104, L.214, E.217, L.218 Ligands: OLC.29 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.104 Hydrogen bonds: C:L.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, H.R. et al., Structural basis for sigma1receptor ligand recognition. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-10-17

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.
Show / Hide

Sigma non-opioid intracellular receptor 1

Related Entries With Identical Sequence