SMTL ID : 6whg.1

PI3P and calcium bound full-length TRPY1 in detergent

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.398, D.401, K.403, D.405 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.398, A:D.401, A:D.401, A:K.403, A:D.405 CA.2: 6 residues within 4Å: Chain A: D.562, T.563, D.566, D.569, Q.591 Chain D: N.161 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.563, A:D.566, A:D.569 CA.4: 4 residues within 4Å: Chain B: D.398, D.401, K.403, D.405 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.398, B:D.401, B:D.401, B:K.403, B:D.405 CA.5: 6 residues within 4Å: Chain A: N.161 Chain B: D.562, T.563, D.566, D.569, Q.591 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.563, B:D.566, B:D.569 CA.7: 4 residues within 4Å: Chain C: D.398, D.401, K.403, D.405 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.398, C:D.401, C:D.401, C:K.403, C:D.405 CA.8: 6 residues within 4Å: Chain B: N.161 Chain C: D.562, T.563, D.566, D.569, Q.591 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.563, C:D.566, C:D.569 CA.10: 4 residues within 4Å: Chain D: D.398, D.401, K.403, D.405 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.398, D:D.401, D:D.401, D:K.403, D:D.405 CA.11: 6 residues within 4Å: Chain C: N.161 Chain D: D.562, T.563, D.566, D.569, Q.591 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.563, D:D.566, D:D.569

4 x PWE: (2R)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1S,2S,3S,4S,5S,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl hexadecanoate(Non-covalent)

PWE.3: 20 residues within 4Å: Chain A: S.297, F.298, W.299, N.300, F.302, P.346, F.347, S.350, L.354, E.357, L.366, L.369, K.370, L.476, Q.479, R.483 Chain D: F.390, I.437, G.441, I.445 17 PLIP interactions: 2 interactions with chain D, 15 interactions with chain A Hydrophobic interactions: D:F.390, D:I.445, A:F.298, A:F.298, A:F.302, A:F.302, A:F.347, A:F.347, A:L.366 Hydrogen bonds: A:S.297, A:F.298, A:W.299, A:N.300, A:E.357, A:Q.479, A:R.483 Salt bridges: A:R.483 PWE.6: 20 residues within 4Å: Chain A: F.390, I.437, G.441, I.445 Chain B: S.297, F.298, W.299, N.300, F.302, P.346, F.347, S.350, L.354, E.357, L.366, L.369, K.370, L.476, Q.479, R.483 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.298, B:F.298, B:F.302, B:F.302, B:F.347, B:F.347, B:L.366, A:F.390, A:I.445 Hydrogen bonds: B:S.297, B:F.298, B:W.299, B:N.300, B:E.357, B:Q.479, B:R.483 Salt bridges: B:R.483 PWE.9: 20 residues within 4Å: Chain B: F.390, I.437, G.441, I.445 Chain C: S.297, F.298, W.299, N.300, F.302, P.346, F.347, S.350, L.354, E.357, L.366, L.369, K.370, L.476, Q.479, R.483 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.298, C:F.298, C:F.302, C:F.302, C:F.347, C:F.347, C:L.366, B:F.390, B:I.445 Hydrogen bonds: C:S.297, C:F.298, C:W.299, C:N.300, C:E.357, C:Q.479, C:R.483 Salt bridges: C:R.483 PWE.12: 20 residues within 4Å: Chain C: F.390, I.437, G.441, I.445 Chain D: S.297, F.298, W.299, N.300, F.302, P.346, F.347, S.350, L.354, E.357, L.366, L.369, K.370, L.476, Q.479, R.483 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.298, D:F.298, D:F.302, D:F.302, D:F.347, D:F.347, D:L.366, C:F.390, C:I.445 Hydrogen bonds: D:S.297, D:F.298, D:W.299, D:N.300, D:E.357, D:Q.479, D:R.483 Salt bridges: D:R.483

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmed, T. et al., Structure of the ancient TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium. Structure (2022)

Release Date

2021-04-21

Peptides

Calcium channel YVC1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Calcium channel YVC1