SMTL ID : 5hk1.1

Human sigma-1 receptor bound to PD144418

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-trimer

Ligands

3 x 61W: 3-(4-methylphenyl)-5-(1-propyl-3,6-dihydro-2H-pyridin-5-yl)-1,2-oxazole(Non-covalent)

61W.1: 15 residues within 4Å: Chain A: V.88, W.93, M.97, Y.107, L.109, F.111, S.121, Y.124, I.128, D.130, H.158, E.176, T.185, L.186, Y.210 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.93, A:L.109, A:F.111, A:F.111, A:I.128, A:H.158, A:L.186, A:Y.210 Hydrogen bonds: A:Y.124 Salt bridges: A:D.130, A:E.176 61W.11: 17 residues within 4Å: Chain B: V.88, W.93, M.97, Y.107, L.109, F.111, S.121, Y.124, I.128, D.130, H.158, W.168, E.176, I.182, T.185, L.186, Y.210 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.93, B:L.109, B:F.111, B:F.111, B:I.128, B:H.158, B:L.186, B:Y.210 Hydrogen bonds: B:Y.124 Salt bridges: B:D.130, B:E.176 61W.16: 15 residues within 4Å: Chain C: V.88, W.93, L.109, F.111, S.121, Y.124, I.128, D.130, H.158, W.168, E.176, I.182, T.185, L.186, Y.210 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.93, C:F.111, C:F.111, C:I.128, C:H.158, C:W.168, C:L.186, C:Y.210 Hydrogen bonds: C:Y.124 Salt bridges: C:D.130, C:E.176

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

SO4.2: 3 residues within 4Å: Chain A: E.82, R.212, R.215 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.82 Water bridges: A:R.208, A:R.215 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:F.41, 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 Water bridges: A:E.59 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 10 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B, 3 interactions with chain A Water bridges: C:G.92, C:R.118, C:R.118, B:G.92, B:R.118, A:R.118, A:R.118 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 SO4.12: 3 residues within 4Å: Chain B: E.82, R.212, R.215 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.82 Water bridges: B:R.215 Salt bridges: B:R.212, B:R.215 SO4.13: 2 residues within 4Å: Chain B: Y.205, R.208 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.208 SO4.14: 3 residues within 4Å: Chain B: Q.42, R.43, R.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.43 Water bridges: B:E.44 Salt bridges: B:R.179 SO4.15: 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 SO4.17: 3 residues within 4Å: Chain C: E.82, R.212, R.215 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.82 Water bridges: C:R.208 Salt bridges: C:R.212, C:R.215 SO4.18: 3 residues within 4Å: Chain C: Q.42, R.43, R.179 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.41, C:R.43 Salt bridges: C:R.179 SO4.19: 1 residues within 4Å: Chain C: R.208 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.208

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

OLC.9: 7 residues within 4Å: Chain A: R.43, W.125, A.126, E.127, P.160, R.179, G.180 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.160 Hydrogen bonds: A:E.127, A:R.179, A:R.179 OLC.10: 6 residues within 4Å: Chain A: L.34, Q.37, F.39, L.104, S.105, G.180 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.104 OLC.20: 6 residues within 4Å: Chain C: L.104, L.214, E.217, Y.221 Ligands: OLC.21, OLC.24 2 PLIP interactions: 2 interactions with chain C Water bridges: C:L.104, C:E.217 OLC.21: 7 residues within 4Å: Chain C: W.33, Q.37, L.104, S.105 Ligands: OLC.20, OLC.22, OLC.24 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.105 Water bridges: C:S.105 OLC.22: 9 residues within 4Å: Chain C: W.33, Q.37, F.39, L.104, S.105, G.180, V.181 Ligands: OLC.21, OLC.23 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.181 Hydrogen bonds: C:Q.37 OLC.23: 5 residues within 4Å: Chain C: W.125, E.127, P.160, R.179 Ligands: OLC.22 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.125, C:W.125 Hydrogen bonds: C:R.179 OLC.24: 4 residues within 4Å: Chain C: W.33, T.36 Ligands: OLC.20, OLC.21 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, H.R. et al., Crystal structure of the human sigma 1 receptor. Nature (2016)

Release Date

2016-04-06

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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