SMTL ID : 5hk2.1

Human sigma-1 receptor bound to 4-IBP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-trimer

Ligands

3 x 61V: N-(1-benzylpiperidin-4-yl)-4-iodobenzamide(Non-covalent)

61V.1: 13 residues within 4Å: Chain A: V.88, W.93, M.97, L.109, F.111, S.121, Y.124, D.130, H.158, E.176, I.182, T.185, Y.210 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.109, A:F.111, A:H.158, A:T.185 Salt bridges: A:D.130, A:E.176 61V.5: 14 residues within 4Å: Chain B: V.88, W.93, M.97, L.109, F.111, S.121, Y.124, D.130, W.168, E.176, T.185, L.186, A.189, Y.210 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.109, B:F.111, B:W.168, B:L.186, B:A.189 Salt bridges: B:D.130, B:E.176 61V.15: 17 residues within 4Å: Chain C: V.88, W.93, M.97, L.109, F.111, S.121, Y.124, I.128, D.130, H.158, W.168, E.176, I.182, T.185, L.186, A.189, Y.210 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.93, C:L.109, C:F.111, C:I.128, C:H.158, C:W.168 Salt bridges: C:D.130, C:E.176

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

SO4.2: 4 residues within 4Å: Chain A: E.82, R.208, R.212, R.215 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.43 Salt bridges: A:R.179 SO4.4: 5 residues within 4Å: Chain A: L.56, D.57, H.58, S.134, N.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.58, A:N.171 Salt bridges: A:H.58 SO4.6: 4 residues within 4Å: Chain B: R.208, R.212, R.215 Ligands: SO4.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.82 Salt bridges: B:R.212, B:R.215 SO4.7: 2 residues within 4Å: Chain B: Y.205, R.208 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.208 SO4.8: 3 residues within 4Å: Chain A: R.118 Chain B: R.118 Chain C: R.118 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:R.118, C:R.118 Salt bridges: A:R.118, B:R.118, C:R.118 SO4.9: 3 residues within 4Å: Chain B: F.204, R.208 Ligands: SO4.6 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.208 SO4.16: 3 residues within 4Å: Chain C: E.82, 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 SO4.17: 3 residues within 4Å: Chain C: Q.42, R.43, R.179 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.42, C:R.43 Salt bridges: C:R.179 SO4.18: 5 residues within 4Å: Chain C: L.56, D.57, H.58, S.134, N.171 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.58, C:N.171 Salt bridges: C:H.58 SO4.19: 1 residues within 4Å: Chain C: R.64 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.64 SO4.20: 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.10: 6 residues within 4Å: Chain B: L.104, L.214, E.217, L.218, Y.221 Ligands: OLC.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.104, B:L.214 Hydrogen bonds: B:E.217, B:E.217 OLC.11: 4 residues within 4Å: Chain B: W.33, Q.37, L.104 Ligands: OLC.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.37 OLC.12: 7 residues within 4Å: Chain B: Q.37, F.39, L.104, S.105, G.180, V.181 Ligands: OLC.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.104, B:V.181 OLC.13: 5 residues within 4Å: Chain B: W.125, E.127, R.179, G.180 Ligands: OLC.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.127, B:E.127, B:R.179 OLC.14: 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:E.59, B:W.85 OLC.21: 5 residues within 4Å: Chain C: W.125, A.126, E.127, R.179, G.180 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.127 OLC.22: 3 residues within 4Å: Chain C: A.54, G.55, P.152 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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