SMTL ID : 9gkb.1

TRPC5 in complex with spin-labelled ligand SpinPico1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 01: 7-[(4-chlorophenyl)methyl]-3-methyl-1-(3-oxidanylpropyl)-8-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)oxy-purine-2,6-dione

01.1: 15 residues within 4Å: Chain A: L.521, Y.524, C.525, L.528, F.569, L.572, Q.573, F.576, W.577 Chain D: F.599, A.602, T.603, G.606, T.607, V.610 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.524, A:F.569, A:L.572, A:L.572 Hydrogen bonds: A:Q.573 pi-Stacking: A:F.576, A:F.576 01.4: 15 residues within 4Å: Chain A: F.599, A.602, T.603, G.606, T.607, V.610 Chain B: L.521, Y.524, C.525, L.528, F.569, L.572, Q.573, F.576, W.577 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.524, B:F.569, B:L.572, B:L.572, A:F.599, A:V.610 Hydrogen bonds: B:Q.573 pi-Stacking: B:F.576, B:F.576 01.7: 15 residues within 4Å: Chain B: F.599, A.602, T.603, G.606, T.607, V.610 Chain C: L.521, Y.524, C.525, L.528, F.569, L.572, Q.573, F.576, W.577 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.524, C:F.569, C:L.572, C:L.572 Hydrogen bonds: C:Q.573 pi-Stacking: C:F.576, C:F.576 01.10: 15 residues within 4Å: Chain C: F.599, A.602, T.603, G.606, T.607, V.610 Chain D: L.521, Y.524, C.525, L.528, F.569, L.572, Q.573, F.576, W.577 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.524, D:F.569, D:L.572, D:L.572 Hydrogen bonds: D:Q.573 pi-Stacking: D:F.576, D:F.576

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.418, Y.430, N.436, D.439, R.492 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.418 CA.5: 5 residues within 4Å: Chain B: E.418, Y.430, N.436, D.439, R.492 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.418 CA.8: 5 residues within 4Å: Chain C: E.418, Y.430, N.436, D.439, R.492 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.418 CA.11: 5 residues within 4Å: Chain D: E.418, E.421, N.436, D.439, R.492 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.418

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 16 residues within 4Å: Chain A: Y.316, F.364, F.367, T.371, L.375, L.378, F.379, S.490, L.493, L.496, F.497, A.499, N.500, S.501 Chain D: L.526, L.529 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.367, A:T.371, A:L.378, A:L.493, A:F.497, A:F.497, A:A.499 Hydrogen bonds: A:S.501 Y01.6: 14 residues within 4Å: Chain A: C.525, L.526, L.529 Chain B: Y.316, F.364, F.367, T.371, L.375, L.493, L.496, F.497, A.499, N.500, S.501 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.367, B:T.371, B:L.375, B:F.497, B:F.497, B:A.499, A:L.526, A:L.529 Hydrogen bonds: B:A.499, B:S.501 Y01.9: 14 residues within 4Å: Chain B: L.526 Chain C: Y.316, F.364, F.367, T.371, L.375, L.378, F.379, L.493, L.496, F.497, A.499, N.500, S.501 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.371, C:L.375, C:L.378, C:L.493, C:F.497, C:F.497, C:A.499, B:L.526 Hydrogen bonds: C:S.501 Y01.12: 15 residues within 4Å: Chain C: L.526, L.529 Chain D: Y.316, W.322, C.334, F.364, F.367, T.371, L.375, L.493, L.496, F.497, A.499, N.500, S.501 11 PLIP interactions: 2 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:L.526, C:L.529, D:L.375, D:L.375, D:L.493, D:L.496, D:F.497, D:A.499, D:N.500 Hydrogen bonds: D:Y.316, D:S.501

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, A.J. et al., Non-covalent spin labelling of TRPC5 ion channels enables EPR studies of protein-ligand interactions. To Be Published

Release Date

2025-09-03

Peptides

Short transient receptor potential channel 5: 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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Short transient receptor potential channel 5

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