SMTL ID : 5irx.1

Structure of TRPV1 in complex with DkTx and RTX, determined in lipid nanodisc

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 2.95 Å

Oligo State

hetero-4-2-mer

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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.335 Hydrogen bonds: A:Y.450 Salt bridges: A:R.386, A:E.408 pi-Cation interactions: A:F.411 6O8.5: 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 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.335 Hydrogen bonds: B:Y.450 Salt bridges: B:R.386, B:E.408 pi-Cation interactions: B:F.411 6O8.8: 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 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.335 Hydrogen bonds: C:Y.450 Salt bridges: C:R.386, C:E.408 pi-Cation interactions: C:F.411 6O8.11: 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 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.335 Hydrogen bonds: D:Y.450 Salt bridges: D:R.386, D:E.408 pi-Cation interactions: D:F.411

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

6OE.2: 8 residues within 4Å: Chain A: L.480, S.501, L.502, Y.503, C.506 Chain C: Y.348 Chain F: A.66, F.67 7 PLIP interactions: 2 interactions with chain A, 4 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: A:Y.503, F:F.67, F:F.67 Hydrogen bonds: A:S.501, F:F.67, F:I.68, C:Y.348 6OE.3: 6 residues within 4Å: Chain A: V.423, L.424, S.427, R.429, E.431 Ligands: 6O9.19 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.423, A:L.424 Salt bridges: A:R.429 6OE.6: 6 residues within 4Å: Chain B: V.423, L.424, S.427, R.429, E.431 Ligands: 6O9.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.423, B:L.424 Salt bridges: B:R.429 6OE.9: 6 residues within 4Å: Chain C: V.423, L.424, S.427, R.429, E.431 Ligands: 6O9.16 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.423, C:L.424 Salt bridges: C:R.429 6OE.13: 8 residues within 4Å: Chain B: Y.348 Chain D: L.480, S.501, L.502, Y.503, C.506 Chain E: A.66, F.67 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: E:F.67, D:S.501, B:Y.348 Hydrophobic interactions: D:L.480, D:Y.503 6OE.14: 6 residues within 4Å: Chain D: V.423, L.424, S.427, R.429, E.431 Ligands: 6O9.12 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.423, D:L.424 Salt bridges: D:R.429 6OE.17: 8 residues within 4Å: Chain C: L.480, S.501, L.502, Y.503, C.506 Chain D: Y.348 Chain E: E.26, F.27 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.480, C:Y.503 Hydrogen bonds: C:S.501, D:Y.348 6OE.20: 8 residues within 4Å: Chain A: Y.348 Chain B: L.480, S.501, L.502, Y.503, C.506 Chain F: E.26, F.27 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: B:Y.503 Hydrogen bonds: B:S.501, A:Y.348, F:I.28

4 x 6EU: resiniferatoxin(Non-covalent)

6EU.4: 21 residues within 4Å: Chain A: Y.406, S.407, I.409, L.410, F.411, A.441, M.442, T.445, N.446, L.448, Y.449, R.452, A.461, I.464, I.468, L.472 Chain B: F.486, A.537, I.540, L.541, L.545 16 PLIP interactions: 5 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:F.486, B:A.537, B:I.540, B:L.541, B:L.541, A:I.409, A:L.410, A:L.410, A:A.441, A:L.448, A:I.464, A:L.472 Hydrogen bonds: A:S.407, A:T.445, A:R.452 pi-Stacking: A:Y.406 6EU.7: 21 residues within 4Å: Chain B: Y.406, S.407, I.409, L.410, F.411, A.441, M.442, T.445, N.446, L.448, Y.449, R.452, A.461, I.464, I.468, L.472 Chain D: F.486, A.537, I.540, L.541, L.545 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:I.409, B:L.410, B:L.410, B:A.441, B:L.448, B:I.464, B:L.472, D:F.486, D:A.537, D:I.540, D:L.541, D:L.541 Hydrogen bonds: B:S.407, B:T.445, B:R.452 pi-Stacking: B:Y.406 6EU.10: 20 residues within 4Å: Chain A: F.486, A.537, I.540, L.541 Chain C: Y.406, S.407, I.409, L.410, F.411, A.441, M.442, T.445, N.446, L.448, Y.449, R.452, A.461, I.464, I.468, L.472 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:I.409, C:L.410, C:L.410, C:L.448, C:I.464, C:L.472, A:F.486, A:A.537, A:I.540, A:L.541, A:L.541 Hydrogen bonds: C:S.407, C:T.445, C:R.452 pi-Stacking: C:Y.406 6EU.15: 20 residues within 4Å: Chain C: F.486, A.537, I.540, L.541 Chain D: Y.406, S.407, I.409, L.410, F.411, A.441, M.442, T.445, N.446, L.448, Y.449, R.452, A.461, I.464, I.468, L.472 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:I.409, D:L.410, D:L.410, D:L.448, D:I.464, D:L.472, C:F.486, C:A.537, C:I.540, C:L.541, C:L.541 Hydrogen bonds: D:S.407, D:T.445, D:R.452 pi-Stacking: D:Y.406

4 x 6O9: (2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl pentanoate(Non-covalent)

6O9.12: 8 residues within 4Å: Chain D: R.429 Chain E: E.49, V.50, W.53, F.67, I.68, Y.70 Ligands: 6OE.14 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:W.53 Hydrogen bonds: E:V.50 Salt bridges: D:R.429 6O9.16: 6 residues within 4Å: Chain C: R.429 Chain E: E.7, V.8, W.11, I.28 Ligands: 6OE.9 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:W.11, E:I.28 Hydrogen bonds: E:V.8 Salt bridges: C:R.429 6O9.18: 6 residues within 4Å: Chain B: R.429 Chain F: E.7, V.8, W.11, I.28 Ligands: 6OE.6 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:I.28 Hydrogen bonds: F:V.8 Salt bridges: B:R.429 6O9.19: 8 residues within 4Å: Chain A: R.429 Chain F: E.49, V.50, W.53, F.67, I.68, Y.70 Ligands: 6OE.3 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:W.53 Hydrogen bonds: F:V.50 Salt bridges: A:R.429

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
Tau-theraphotoxin-Hs1a: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

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

Tau-theraphotoxin-Hs1a

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