SMTL ID : 6dk0.1

Human sigma-1 receptor bound to NE-100

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-trimer

Ligands

3 x GKY: N-{2-[4-methoxy-3-(2-phenylethoxy)phenyl]ethyl}-N-propylpropan-1-amine(Non-covalent)

GKY.1: 18 residues within 4Å: Chain A: V.88, W.93, Y.107, L.109, F.111, S.121, Y.124, I.128, D.130, F.137, H.158, W.168, M.174, E.176, I.182, T.185, A.189, Y.210 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.88, A:W.93, A:Y.107, A:F.111, A:Y.124, A:I.128, A:I.128, A:F.137, A:H.158, A:W.168, A:I.182, A:Y.210 Hydrogen bonds: A:T.185 Salt bridges: A:D.130, A:E.176 GKY.12: 17 residues within 4Å: Chain B: V.88, M.97, L.99, Y.107, S.121, Y.124, I.128, D.130, F.137, H.158, W.168, E.176, I.182, T.185, L.186, A.189, Y.210 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.88, B:L.99, B:Y.124, B:I.128, B:F.137, B:H.158, B:W.168, B:I.182, B:L.186, B:Y.210, B:Y.210 Hydrogen bonds: B:Y.124, B:T.185 Salt bridges: B:D.130, B:E.176 GKY.19: 18 residues within 4Å: Chain C: V.88, M.97, L.99, Y.107, L.109, S.121, Y.124, I.128, D.130, H.158, V.166, W.168, E.176, I.182, L.186, A.189, T.206, Y.210 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:V.88, C:L.99, C:L.99, C:Y.107, C:Y.124, C:I.128, C:H.158, C:V.166, C:W.168, C:I.182, C:L.186, C:T.206, C:Y.210, C:Y.210 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.82 Water bridges: A:R.208, A:R.215, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: 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: 1 residues within 4Å: Chain A: R.64 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.64 SO4.7: 1 residues within 4Å: Chain A: R.141 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.141 SO4.13: 3 residues within 4Å: Chain B: E.82, R.212, R.215 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.82 Salt bridges: B:R.212, B:R.215 SO4.14: 1 residues within 4Å: Chain B: R.208 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.208 SO4.15: 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 SO4.16: 4 residues within 4Å: Chain B: L.56, D.57, H.58, S.134 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.58, B:S.134 Water bridges: B:G.135 Salt bridges: B:H.58 SO4.17: 3 residues within 4Å: Chain A: R.118 Chain B: R.118 Chain C: R.118 8 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 4 interactions with chain A Water bridges: B:R.118, C:G.92, A:R.118, A:R.118, A:R.118 Salt bridges: B:R.118, C:R.118, A:R.118 SO4.20: 4 residues within 4Å: Chain C: E.82, R.208, 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 SO4.21: 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 SO4.22: 1 residues within 4Å: Chain C: R.208 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.208

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: F.62, L.83, W.85, C.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.83, A:W.85 Water bridges: A:W.85 GOL.18: 1 residues within 4Å: Chain B: W.85 No protein-ligand interaction detected (PLIP) GOL.23: 1 residues within 4Å: Chain C: W.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.85

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

OLC.9: 3 residues within 4Å: Chain A: L.34, L.104, V.181 No protein-ligand interaction detected (PLIP) OLC.10: 4 residues within 4Å: Chain A: R.123, Y.124, W.125, S.184 No protein-ligand interaction detected (PLIP) OLC.11: 5 residues within 4Å: Chain A: R.43, A.126, P.160, R.179, G.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.127 OLC.24: 7 residues within 4Å: Chain C: W.33, Q.37, L.104, S.105, G.180, V.181 Ligands: OLC.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.37 OLC.25: 3 residues within 4Å: Chain C: W.33 Ligands: OLC.24, OLC.27 No protein-ligand interaction detected (PLIP) OLC.26: 4 residues within 4Å: Chain C: S.103, L.214, E.217, L.218 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.217 OLC.27: 3 residues within 4Å: Chain C: W.33, T.36 Ligands: OLC.25 No protein-ligand interaction detected (PLIP) OLC.28: 5 residues within 4Å: Chain C: W.125, E.127, P.160, R.179, G.180 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.127

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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