SMTL ID : 6o6r.1

Structure of the TRPM8 cold receptor by single particle electron cryo-microscopy, AMTB-bound state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 13 residues within 4Å: Chain A: W.677, I.691, F.730, F.733, S.734, V.737, I.738, I.741, S.844, L.847, R.992, V.996 Ligands: 9PE.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.677, A:W.677, A:I.691, A:I.691, A:I.691, A:F.730, A:F.733, A:V.737, A:I.738, A:I.741 Salt bridges: A:R.992 Y01.8: 13 residues within 4Å: Chain B: W.677, I.691, F.730, F.733, S.734, V.737, I.738, I.741, S.844, L.847, R.992, V.996 Ligands: 9PE.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.677, B:W.677, B:I.691, B:I.691, B:I.691, B:F.730, B:F.733, B:V.737, B:I.738, B:I.741 Salt bridges: B:R.992 Y01.15: 13 residues within 4Å: Chain C: W.677, I.691, F.730, F.733, S.734, V.737, I.738, I.741, S.844, L.847, R.992, V.996 Ligands: 9PE.17 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.677, C:W.677, C:I.691, C:I.691, C:I.691, C:F.730, C:F.733, C:V.737, C:I.738, C:I.741 Salt bridges: C:R.992 Y01.22: 13 residues within 4Å: Chain D: W.677, I.691, F.730, F.733, S.734, V.737, I.738, I.741, S.844, L.847, R.992, V.996 Ligands: 9PE.24 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.677, D:W.677, D:I.691, D:I.691, D:I.691, D:F.730, D:F.733, D:V.737, D:I.738, D:I.741 Salt bridges: D:R.992

8 x UND: UNDECANE(Covalent)(Non-covalent)

UND.2: 6 residues within 4Å: Chain A: N.687, W.688, I.691, M.692, F.695 Ligands: 9PE.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.688, A:F.695 UND.4: 5 residues within 4Å: Chain A: F.868, M.905 Chain D: Y.957, T.961, L.965 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.868, D:T.961, D:L.965 UND.9: 6 residues within 4Å: Chain B: N.687, W.688, I.691, M.692, F.695 Ligands: 9PE.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.688, B:F.695 UND.11: 5 residues within 4Å: Chain A: Y.957, T.961, L.965 Chain B: F.868, M.905 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.961, A:L.965, B:F.868 UND.16: 6 residues within 4Å: Chain C: N.687, W.688, I.691, M.692, F.695 Ligands: 9PE.17 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.688, C:F.695 UND.18: 5 residues within 4Å: Chain B: Y.957, T.961, L.965 Chain C: F.868, M.905 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.961, B:L.965, C:F.868 UND.23: 6 residues within 4Å: Chain D: N.687, W.688, I.691, M.692, F.695 Ligands: 9PE.24 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.688, D:F.695 UND.25: 5 residues within 4Å: Chain C: Y.957, T.961, L.965 Chain D: F.868, M.905 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.961, C:L.965, D:F.868

4 x 9PE: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate(Non-covalent)

9PE.3: 12 residues within 4Å: Chain A: N.687, I.741, L.745, Y.830, S.844, R.845, L.847 Chain D: F.863, F.866, V.873 Ligands: Y01.1, UND.2 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:I.741, A:L.745, D:F.863, D:F.866, D:F.866, D:V.873 Hydrogen bonds: A:N.687, A:R.845 9PE.10: 11 residues within 4Å: Chain A: F.866, V.873 Chain B: N.687, I.741, L.745, Y.830, S.844, R.845, L.847 Ligands: Y01.8, UND.9 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.741, B:L.745, A:F.866, A:F.866, A:V.873 Hydrogen bonds: B:N.687, B:R.845 9PE.17: 10 residues within 4Å: Chain B: F.866 Chain C: N.687, I.741, L.745, Y.830, S.844, R.845, L.847 Ligands: Y01.15, UND.16 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.741, C:L.745, B:F.866, B:F.866 Hydrogen bonds: C:N.687, C:R.845 9PE.24: 12 residues within 4Å: Chain C: F.863, F.866, V.873 Chain D: N.687, I.741, L.745, Y.830, S.844, R.845, L.847 Ligands: Y01.22, UND.23 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.741, D:L.745, C:F.863, C:F.866, C:F.866, C:V.873 Hydrogen bonds: D:N.687, D:R.845

4 x LQ7: N-(3-aminopropyl)-2-[(3-methylphenyl)methoxy]-N-[(thiophen-2-yl)methyl]benzamide(Non-covalent)

LQ7.5: 12 residues within 4Å: Chain A: F.733, N.736, V.737, Y.740, L.773, E.777, N.794, D.797, F.833, R.836, I.840, R.1002 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.733, A:N.736, A:V.737, A:Y.740, A:L.773, A:D.797, A:F.833, A:I.840 Hydrogen bonds: A:R.836 pi-Cation interactions: A:R.836 LQ7.12: 12 residues within 4Å: Chain B: F.733, N.736, V.737, Y.740, L.773, E.777, N.794, D.797, F.833, R.836, I.840, R.1002 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.733, B:N.736, B:V.737, B:Y.740, B:L.773, B:D.797, B:F.833, B:I.840 Hydrogen bonds: B:R.836 pi-Cation interactions: B:R.836 LQ7.19: 12 residues within 4Å: Chain C: F.733, N.736, V.737, Y.740, L.773, E.777, N.794, D.797, F.833, R.836, I.840, R.1002 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.733, C:N.736, C:V.737, C:Y.740, C:L.773, C:D.797, C:F.833, C:I.840 Hydrogen bonds: C:R.836 pi-Cation interactions: C:R.836 LQ7.26: 12 residues within 4Å: Chain D: F.733, N.736, V.737, Y.740, L.773, E.777, N.794, D.797, F.833, R.836, I.840, R.1002 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.733, D:N.736, D:V.737, D:Y.740, D:L.773, D:D.797, D:F.833, D:I.840 Hydrogen bonds: D:R.836 pi-Cation interactions: D:R.836

8 x NA: SODIUM ION(Non-functional Binders)

NA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.7: 1 residues within 4Å: Chain A: W.871 No protein-ligand interaction detected (PLIP) NA.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.14: 1 residues within 4Å: Chain B: W.871 No protein-ligand interaction detected (PLIP) NA.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.21: 1 residues within 4Å: Chain C: W.871 No protein-ligand interaction detected (PLIP) NA.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.28: 1 residues within 4Å: Chain D: W.871 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diver, M.M. et al., Structural insights into TRPM8 inhibition and desensitization. Science (2019)

Release Date

2019-09-18

Peptides

Transient receptor potential cation channel subfamily M member 8: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily M member 8

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