SMTL ID : 5irz.1

Structure of TRPV1 determined in lipid nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.28 Å

Oligo State

homo-tetramer

Ligands

4 x 6O8: (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium(Covalent)

6O8.1: 14 residues within 4Å: Chain A: N.332, V.335, Y.336, Y.339, S.378, G.379, Y.382, F.383, R.386, S.407, E.408, F.411, Y.449, Y.450 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.335 Hydrogen bonds: A:Y.382 Salt bridges: A:R.386, A:E.408 6O8.7: 14 residues within 4Å: Chain B: N.332, V.335, Y.336, Y.339, S.378, G.379, Y.382, F.383, R.386, S.407, E.408, F.411, Y.449, Y.450 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.335 Hydrogen bonds: B:Y.382 Salt bridges: B:R.386, B:E.408 6O8.13: 14 residues within 4Å: Chain C: N.332, V.335, Y.336, Y.339, S.378, G.379, Y.382, F.383, R.386, S.407, E.408, F.411, Y.449, Y.450 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.335 Hydrogen bonds: C:Y.382 Salt bridges: C:R.386, C:E.408 6O8.19: 14 residues within 4Å: Chain D: N.332, V.335, Y.336, Y.339, S.378, G.379, Y.382, F.383, R.386, S.407, E.408, F.411, Y.449, Y.450 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.335 Hydrogen bonds: D:Y.382 Salt bridges: D:R.386, D:E.408

4 x 6ES: (2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(pentanoyloxy)propan-2-yl decanoate(Covalent)

6ES.2: 22 residues within 4Å: Chain A: H.305, V.403, D.404, S.405, Y.406, S.407, E.408, L.410, M.442, T.445, L.448, Y.449, R.452, E.465, I.468, L.469, I.568, L.571, Q.572, I.575 Chain B: F.486, L.541 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.410, A:I.468 Hydrogen bonds: A:V.403, A:V.403, A:Y.406, A:S.407, A:S.407, A:E.408, A:K.466, A:Q.572 Salt bridges: A:R.452 6ES.8: 22 residues within 4Å: Chain B: H.305, V.403, D.404, S.405, Y.406, S.407, E.408, L.410, M.442, T.445, L.448, Y.449, R.452, E.465, I.468, L.469, I.568, L.571, Q.572, I.575 Chain D: F.486, L.541 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.410, B:I.468 Hydrogen bonds: B:V.403, B:V.403, B:Y.406, B:S.407, B:S.407, B:E.408, B:K.466, B:Q.572 Salt bridges: B:R.452 6ES.14: 22 residues within 4Å: Chain A: F.486, L.541 Chain C: H.305, V.403, D.404, S.405, Y.406, S.407, E.408, L.410, M.442, T.445, L.448, Y.449, R.452, E.465, I.468, L.469, I.568, L.571, Q.572, I.575 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.410, C:I.468 Hydrogen bonds: C:V.403, C:V.403, C:Y.406, C:S.407, C:S.407, C:E.408, C:K.466, C:Q.572 Salt bridges: C:R.452 6ES.20: 22 residues within 4Å: Chain C: F.486, L.541 Chain D: H.305, V.403, D.404, S.405, Y.406, S.407, E.408, L.410, M.442, T.445, L.448, Y.449, R.452, E.465, I.468, L.469, I.568, L.571, Q.572, I.575 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.410, D:I.468 Hydrogen bonds: D:V.403, D:V.403, D:Y.406, D:S.407, D:S.407, D:E.408, D:K.466, D:Q.572 Salt bridges: D:R.452

16 x 6OE: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate(Non-covalent)

6OE.3: 8 residues within 4Å: Chain A: Y.503 Chain B: K.528, A.529, I.532, I.533, L.536 Ligands: 6OE.9, 6OE.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.503 6OE.4: 6 residues within 4Å: Chain A: F.527, A.529, V.530, I.533 Chain C: F.438 Ligands: 6OE.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.529 6OE.5: 11 residues within 4Å: Chain A: I.341, T.344, A.345, Y.348, Y.349 Chain B: F.484, N.500, S.501, L.502 Ligands: 6OE.6, 6OE.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.344, B:F.484 Hydrogen bonds: A:Y.348 6OE.6: 7 residues within 4Å: Chain A: A.345, A.346, Y.349, G.365, F.368, R.369 Ligands: 6OE.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.349, A:R.369 6OE.9: 7 residues within 4Å: Chain A: F.438 Chain B: F.527, K.528, A.529, V.530, I.533 Ligands: 6OE.3 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.529 6OE.10: 11 residues within 4Å: Chain B: I.341, T.344, A.345, Y.348, Y.349 Chain D: F.484, N.500, S.501, L.502 Ligands: 6OE.11, 6OE.23 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:F.484, B:T.344 Hydrogen bonds: B:Y.348 6OE.11: 7 residues within 4Å: Chain B: A.345, A.346, Y.349, G.365, F.368, R.369 Ligands: 6OE.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.349, B:R.369 6OE.12: 8 residues within 4Å: Chain B: Y.503 Chain D: K.528, A.529, I.532, I.533, L.536 Ligands: 6OE.5, 6OE.24 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.503 6OE.15: 11 residues within 4Å: Chain A: F.484, N.500, S.501, L.502 Chain C: I.341, T.344, A.345, Y.348, Y.349 Ligands: 6OE.3, 6OE.16 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:T.344, A:F.484 Hydrogen bonds: C:Y.348 6OE.16: 7 residues within 4Å: Chain C: A.345, A.346, Y.349, G.365, F.368, R.369 Ligands: 6OE.15 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.349, C:R.369 6OE.17: 8 residues within 4Å: Chain A: K.528, A.529, I.532, I.533, L.536 Chain C: Y.503 Ligands: 6OE.4, 6OE.21 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.503 6OE.18: 6 residues within 4Å: Chain C: F.527, A.529, V.530, I.533 Chain D: F.438 Ligands: 6OE.23 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.529 6OE.21: 11 residues within 4Å: Chain C: F.484, N.500, S.501, L.502 Chain D: I.341, T.344, A.345, Y.348, Y.349 Ligands: 6OE.17, 6OE.22 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:T.344, C:F.484 Hydrogen bonds: D:Y.348 6OE.22: 7 residues within 4Å: Chain D: A.345, A.346, Y.349, G.365, F.368, R.369 Ligands: 6OE.21 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.349, D:R.369 6OE.23: 8 residues within 4Å: Chain C: K.528, A.529, I.532, I.533, L.536 Chain D: Y.503 Ligands: 6OE.10, 6OE.18 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.503 Hydrogen bonds: D:S.501 6OE.24: 6 residues within 4Å: Chain B: F.438 Chain D: F.527, A.529, V.530, I.533 Ligands: 6OE.12 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.529

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Y. et al., TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action. Nature (2016)

Release Date

2016-05-25

Peptides

Transient receptor potential cation channel subfamily V member 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
B

D
C

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily V member 1

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