SMTL ID : 6dk1.1

Human sigma-1 receptor bound to (+)-pentazocine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.12 Å

Oligo State

homo-trimer

Ligands

3 x GM4: (2S,6S,11S)-6,11-dimethyl-3-(3-methylbut-2-en-1-yl)-1,2,3,4,5,6-hexahydro-2,6-methano-3-benzazocin-8-ol(Non-covalent)

GM4.1: 13 residues within 4Å: Chain A: V.88, A.90, W.93, M.97, Y.107, L.109, F.111, Y.124, D.130, W.168, E.176, F.188, A.189 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.90, A:Y.107, A:L.109, A:W.168, A:F.188, A:A.189 Salt bridges: A:E.176 GM4.12: 13 residues within 4Å: Chain B: V.88, A.90, W.93, Y.107, L.109, F.111, Y.124, D.130, W.168, E.176, F.188, A.189, L.190 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.90, B:W.93, B:W.93, B:W.168, B:F.188 Salt bridges: B:D.130, B:E.176 GM4.21: 12 residues within 4Å: Chain C: V.88, A.90, W.93, Y.107, L.109, F.111, Y.124, D.130, W.168, E.176, T.185, A.189 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.88, C:A.90, C:W.93, C:W.93, C:W.168, C:A.189 Salt bridges: C:E.176

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

SO4.2: 2 residues within 4Å: Chain A: R.212, R.215 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.215, A:R.215 Salt bridges: A:R.212, A:R.215 SO4.3: 4 residues within 4Å: Chain A: L.56, D.57, H.58, N.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.58 Salt bridges: A:H.58 SO4.4: 1 residues within 4Å: Chain A: R.208 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.208 SO4.5: 2 residues within 4Å: Chain A: Q.52, R.64 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.64 SO4.6: 2 residues within 4Å: Chain A: R.141, T.144 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.141 SO4.7: 3 residues within 4Å: Chain A: Q.42, R.43, R.179 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.43, A:R.179 SO4.8: 3 residues within 4Å: Chain A: R.118 Chain B: R.118 Chain C: R.118 8 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 3 interactions with chain C Water bridges: B:G.92, B:R.118, A:R.118, C:R.118, C:R.118 Salt bridges: B:R.118, A:R.118, C:R.118 SO4.13: 1 residues within 4Å: Chain B: R.212 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.212, B:R.215 SO4.14: 2 residues within 4Å: Chain B: Y.205, R.208 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.205 Salt bridges: B:R.208 SO4.15: 2 residues within 4Å: Chain B: H.58, S.134 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.58, B:S.134, B:S.134 Salt bridges: B:H.58 SO4.16: 5 residues within 4Å: Chain B: F.39, F.41, Q.42, R.43, R.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.43 Salt bridges: B:R.179 SO4.22: 2 residues within 4Å: Chain C: R.212, R.215 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.208 Salt bridges: C:R.212, C:R.215 SO4.23: 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 SO4.24: 1 residues within 4Å: Chain C: R.208 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.208

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: L.83, W.85, C.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.83 GOL.17: 4 residues within 4Å: Chain B: E.59, L.83, W.85, C.98 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.83, B:W.85 GOL.25: 5 residues within 4Å: Chain C: E.59, I.66, L.83, W.85 Ligands: GOL.26 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.59, C:L.83 GOL.26: 3 residues within 4Å: Chain C: D.80, L.83 Ligands: GOL.25 No protein-ligand interaction detected (PLIP)

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

OLC.10: 4 residues within 4Å: Chain A: W.33, S.103, L.104, L.214 No protein-ligand interaction detected (PLIP) OLC.11: 4 residues within 4Å: Chain A: L.34, Q.37, L.104, S.105 No protein-ligand interaction detected (PLIP) OLC.18: 1 residues within 4Å: Ligands: OLC.19 No protein-ligand interaction detected (PLIP) OLC.19: 4 residues within 4Å: Chain B: L.104, S.105, V.181 Ligands: OLC.18 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.104, B:L.104 OLC.20: 5 residues within 4Å: Chain B: W.125, E.127, P.160, G.180, V.181 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.181 Hydrogen bonds: B:E.127, B:E.127, B:V.181 OLC.27: 4 residues within 4Å: Chain C: R.43, W.125, E.127, R.179 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.125 Hydrogen bonds: C:E.127, C:R.179, C:R.179 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: 3 residues within 4Å: Chain C: W.33, T.36 Ligands: OLC.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.36, C:T.36 OLC.30: 6 residues within 4Å: Chain C: W.33, Q.37, L.104, S.105 Ligands: OLC.29, OLC.31 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.37, C:S.105 OLC.31: 5 residues within 4Å: Chain C: S.103, L.104, L.214, E.217 Ligands: OLC.30 No protein-ligand interaction detected (PLIP) OLC.32: 3 residues within 4Å: Chain C: L.218, T.219, F.223 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.218, C:T.219

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.
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Sigma non-opioid intracellular receptor 1

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