SMTL ID : 6o72.1

Structure of the TRPM8 cold receptor by single particle electron cryo-microscopy, TC-I 2014-bound state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x Y01: CHOLESTEROL HEMISUCCINATE(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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.677, A:I.691, A:F.730, A:F.733, A:V.737, A:I.738, A:I.738, A:I.741, A:L.847 Salt bridges: A:R.992 Y01.9: 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.11 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.677, B:I.691, B:F.730, B:F.733, B:V.737, B:I.738, B:I.738, B:I.741, B:L.847 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 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.677, C:I.691, C:F.730, C:F.733, C:V.737, C:I.738, C:I.738, C:I.741, C:L.847 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 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.677, D:I.691, D:F.730, D:F.733, D:V.737, D:I.738, D:I.738, D:I.741, D:L.847 Salt bridges: D:R.992

8 x UND: UNDECANE(Non-covalent)

UND.2: 5 residues within 4Å: Chain A: N.687, W.688, I.691, F.695 Ligands: 9PE.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.687, A:W.688, A:I.691, A:I.691, A:F.695, A:F.695 UND.4: 4 residues within 4Å: Chain A: F.868, L.968 Chain D: Y.957, L.965 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.868, A:L.968, D:Y.957, D:L.965 UND.8: 4 residues within 4Å: Chain A: Y.957, L.965 Chain B: F.868, L.968 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.868, B:L.968, A:Y.957, A:L.965 UND.10: 5 residues within 4Å: Chain B: N.687, W.688, I.691, F.695 Ligands: 9PE.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:N.687, B:W.688, B:I.691, B:I.691, B:F.695, B:F.695 UND.16: 5 residues within 4Å: Chain C: N.687, W.688, I.691, F.695 Ligands: 9PE.17 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:N.687, C:W.688, C:I.691, C:I.691, C:F.695, C:F.695 UND.18: 4 residues within 4Å: Chain B: Y.957, L.965 Chain C: F.868, L.968 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.868, C:L.968, B:Y.957, B:L.965 UND.23: 5 residues within 4Å: Chain D: N.687, W.688, I.691, F.695 Ligands: 9PE.24 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:N.687, D:W.688, D:I.691, D:I.691, D:F.695, D:F.695 UND.25: 4 residues within 4Å: Chain C: Y.957, L.965 Chain D: F.868, L.968 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.868, D:L.968, C:Y.957, C:L.965

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

9PE.3: 11 residues within 4Å: Chain A: N.687, I.741, L.837, F.841, S.844, R.845, L.847 Chain D: F.863, F.866 Ligands: Y01.1, UND.2 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:F.863, D:F.866, A:L.837, A:F.841, A:F.841 Hydrogen bonds: A:N.687, A:L.847 9PE.11: 10 residues within 4Å: Chain A: F.866 Chain B: N.687, I.741, L.837, F.841, S.844, R.845, L.847 Ligands: Y01.9, UND.10 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.837, B:F.841, B:F.841, A:F.866 Hydrogen bonds: B:N.687, B:L.847 9PE.17: 11 residues within 4Å: Chain B: F.863, F.866 Chain C: N.687, I.741, L.837, F.841, S.844, R.845, L.847 Ligands: Y01.15, UND.16 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:F.863, B:F.866, C:L.837, C:F.841, C:F.841 Hydrogen bonds: C:N.687, C:L.847 9PE.24: 11 residues within 4Å: Chain C: F.863, F.866 Chain D: N.687, I.741, L.837, F.841, S.844, R.845, L.847 Ligands: Y01.22, UND.23 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.863, C:F.866, D:L.837, D:F.841, D:F.841 Hydrogen bonds: D:N.687, D:L.847

4 x T14: 3-{7-(trifluoromethyl)-5-[2-(trifluoromethyl)phenyl]-1H-benzimidazol-2-yl}-1-oxa-2-azaspiro[4.5]dec-2-ene(Non-covalent)

T14.5: 13 residues within 4Å: Chain A: F.733, Y.740, L.773, N.794, D.797, I.801, R.836, I.840, V.843, S.844, L.847, Y.999, R.1002 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.733, A:Y.740, A:D.797, A:I.801, A:R.836, A:L.847, A:Y.999, A:Y.999 Hydrogen bonds: A:R.836, A:R.836, A:R.1002 T14.12: 13 residues within 4Å: Chain B: F.733, Y.740, L.773, N.794, D.797, I.801, R.836, I.840, V.843, S.844, L.847, Y.999, R.1002 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.733, B:Y.740, B:D.797, B:I.801, B:R.836, B:L.847, B:Y.999, B:Y.999 Hydrogen bonds: B:R.836, B:R.836, B:R.1002 T14.19: 13 residues within 4Å: Chain C: F.733, Y.740, L.773, N.794, D.797, I.801, R.836, I.840, V.843, S.844, L.847, Y.999, R.1002 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.733, C:Y.740, C:D.797, C:I.801, C:R.836, C:L.847, C:Y.999, C:Y.999 Hydrogen bonds: C:R.836, C:R.836, C:R.1002 T14.26: 13 residues within 4Å: Chain D: F.733, Y.740, L.773, N.794, D.797, I.801, R.836, I.840, V.843, S.844, L.847, Y.999, R.1002 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.733, D:Y.740, D:D.797, D:I.801, D:R.836, D:L.847, D:Y.999, D:Y.999 Hydrogen bonds: D:R.836, D:R.836, D:R.1002

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: T.961 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: T.961 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.961 NA.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.21: 1 residues within 4Å: Chain C: T.961 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: T.961 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.961

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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