SMTL ID : 8bdc.1

Human apo TRPM8 in a closed state (composite map)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 13 residues within 4Å: Chain A: W.683, I.697, F.701, F.736, F.739, V.743, V.744, S.851, L.854, R.999, V.1003 Ligands: POV.2, Y01.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.683, A:I.697, A:F.736, A:F.739, A:V.743, A:V.744, A:L.854, A:V.1003 Salt bridges: A:R.999 Y01.3: 7 residues within 4Å: Chain A: N.693, W.694, I.697, L.698, F.701 Ligands: Y01.1, POV.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.693, A:F.701, A:F.701, A:F.701 Y01.7: 13 residues within 4Å: Chain B: W.683, I.697, F.701, F.736, F.739, V.743, V.744, S.851, L.854, R.999, V.1003 Ligands: POV.8, Y01.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.683, B:I.697, B:F.736, B:F.739, B:V.743, B:V.744, B:L.854, B:V.1003 Salt bridges: B:R.999 Y01.9: 7 residues within 4Å: Chain B: N.693, W.694, I.697, L.698, F.701 Ligands: Y01.7, POV.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.693, B:F.701, B:F.701, B:F.701 Y01.13: 13 residues within 4Å: Chain C: W.683, I.697, F.701, F.736, F.739, V.743, V.744, S.851, L.854, R.999, V.1003 Ligands: POV.14, Y01.15 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.683, C:I.697, C:F.736, C:F.739, C:V.743, C:V.744, C:L.854, C:V.1003 Salt bridges: C:R.999 Y01.15: 7 residues within 4Å: Chain C: N.693, W.694, I.697, L.698, F.701 Ligands: Y01.13, POV.14 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:N.693, C:F.701, C:F.701, C:F.701 Y01.19: 13 residues within 4Å: Chain D: W.683, I.697, F.701, F.736, F.739, V.743, V.744, S.851, L.854, R.999, V.1003 Ligands: POV.20, Y01.21 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.683, D:I.697, D:F.736, D:F.739, D:V.743, D:V.744, D:L.854, D:V.1003 Salt bridges: D:R.999 Y01.21: 7 residues within 4Å: Chain D: N.693, W.694, I.697, L.698, F.701 Ligands: Y01.19, POV.20 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:N.693, D:F.701, D:F.701, D:F.701

4 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.2: 13 residues within 4Å: Chain A: Y.684, N.693, I.747, Y.837, T.841, L.844, F.848, S.851, R.852 Chain B: F.870, F.873 Ligands: Y01.1, Y01.3 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.747, A:T.841, A:F.848, A:F.848, A:F.848, B:F.870, B:F.873 POV.8: 14 residues within 4Å: Chain B: Y.684, N.693, I.747, Y.837, T.841, L.844, F.848, S.851, R.852 Chain C: F.870, F.873, V.880 Ligands: Y01.7, Y01.9 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:F.870, C:F.873, C:V.880, B:I.747, B:T.841, B:F.848, B:F.848, B:F.848 POV.14: 13 residues within 4Å: Chain C: Y.684, N.693, I.747, Y.837, T.841, L.844, F.848, S.851, R.852 Chain D: F.870, F.873 Ligands: Y01.13, Y01.15 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.747, C:T.841, C:F.848, C:F.848, C:F.848, D:F.870, D:F.873 POV.20: 14 residues within 4Å: Chain A: F.870, F.873, V.880 Chain D: Y.684, N.693, I.747, Y.837, T.841, L.844, F.848, S.851, R.852 Ligands: Y01.19, Y01.21 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:F.870, A:F.873, A:V.880, D:I.747, D:T.841, D:F.848, D:F.848, D:F.848

4 x UND: UNDECANE(Non-covalent)

UND.4: 5 residues within 4Å: Chain A: L.872, F.875 Chain B: M.965, T.968, L.972 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.968, B:L.972, A:L.872, A:F.875 UND.10: 5 residues within 4Å: Chain B: L.872, F.875 Chain C: M.965, T.968, L.972 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.872, B:F.875, C:T.968, C:L.972 UND.16: 5 residues within 4Å: Chain C: L.872, F.875 Chain D: M.965, T.968, L.972 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:T.968, D:L.972, C:L.872, C:F.875 UND.22: 5 residues within 4Å: Chain A: M.965, T.968, L.972 Chain D: L.872, F.875 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.872, D:F.875, A:T.968, A:L.972

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

NA.5: 1 residues within 4Å: Chain A: L.971 No protein-ligand interaction detected (PLIP) NA.6: 2 residues within 4Å: Chain A: W.878, S.967 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.967, A:T.968 NA.11: 1 residues within 4Å: Chain B: L.971 No protein-ligand interaction detected (PLIP) NA.12: 2 residues within 4Å: Chain B: W.878, S.967 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.967, B:S.967 NA.17: 1 residues within 4Å: Chain C: L.971 No protein-ligand interaction detected (PLIP) NA.18: 2 residues within 4Å: Chain C: W.878, S.967 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.967, C:S.967 NA.23: 1 residues within 4Å: Chain D: L.971 No protein-ligand interaction detected (PLIP) NA.24: 2 residues within 4Å: Chain D: W.878, S.967 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.967, D:S.967

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palchevskyi, S. et al., Structure of human TRPM8 channel. Commun Biol (2023)

Release Date

2023-11-01

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