SMTL ID : 7l2x.1

cryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state c

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 6EU: resiniferatoxin(Non-covalent)

6EU.1: 17 residues within 4Å: Chain A: Y.407, S.408, L.411, F.412, M.443, T.446, N.447, L.449, Y.450, R.453, A.462, I.465, I.469 Chain B: F.483, F.487, I.541, L.542 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.411, A:L.411, B:F.487, B:I.541, B:L.542, B:L.542 Hydrogen bonds: A:S.408, A:T.446 pi-Stacking: A:Y.407 6EU.4: 19 residues within 4Å: Chain B: Y.407, S.408, L.411, F.412, A.442, M.443, T.446, N.447, L.449, Y.450, R.453, A.462, I.465, I.469 Chain D: F.483, F.487, A.538, I.541, L.542 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:L.411, B:L.411, D:F.487, D:A.538, D:I.541, D:L.542, D:L.542 Hydrogen bonds: B:S.408, B:T.446, B:R.453 pi-Stacking: B:Y.407 6EU.7: 18 residues within 4Å: Chain A: F.483, F.487, A.538, I.541, L.542 Chain C: Y.407, S.408, L.411, F.412, A.442, M.443, T.446, N.447, L.449, Y.450, R.453, A.462, I.465 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.411, C:L.411, C:A.462, A:F.487, A:A.538, A:I.541, A:L.542 Hydrogen bonds: C:S.408, C:T.446, C:R.453 pi-Stacking: C:Y.407 6EU.9: 17 residues within 4Å: Chain C: F.483, F.487, I.541, L.542 Chain D: Y.407, S.408, L.411, F.412, M.443, T.446, N.447, L.449, Y.450, R.453, A.462, I.465, I.469 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.411, D:L.411, D:A.462, C:F.487, C:I.541 Hydrogen bonds: D:S.408, D:T.446, D:R.453 pi-Stacking: D:Y.407

4 x 6IY: (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate(Non-covalent)

6IY.2: 7 residues within 4Å: Chain A: Y.504, S.505, L.508, F.511 Chain B: A.530, I.533, I.534 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.504, A:L.508, A:F.511, B:A.530, B:I.534 Hydrogen bonds: A:S.505 6IY.3: 10 residues within 4Å: Chain A: K.529, A.530, I.533, I.534 Chain C: M.477, Y.480, Y.504, C.507, L.508, F.511 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.480, C:Y.504, C:F.511, C:F.511, A:I.533, A:I.534 Salt bridges: A:K.529 6IY.5: 10 residues within 4Å: Chain B: M.477, Y.480, Y.504, S.505, L.508, F.511 Chain D: K.529, A.530, I.533, I.534 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:Y.480, B:Y.504, B:Y.504, B:L.508, B:F.511, D:I.534 Salt bridges: D:K.529, D:K.529 6IY.8: 9 residues within 4Å: Chain C: A.530, I.533, I.534, L.537, I.541 Chain D: M.477, Y.480, Y.504, L.508 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:Y.480, D:Y.504, D:L.508, C:I.534, C:L.537, C:I.541 Salt bridges: C:K.529, C:K.529

1 x XPJ: 1-deoxy-1-(methylamino)-D-allitol(Non-covalent)

XPJ.6: 10 residues within 4Å: Chain A: G.516 Chain B: G.516, M.517 Chain C: G.516, M.517, G.518, Y.544 Chain D: G.516, M.517, G.518 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.516, C:Y.544, C:Y.544, B:G.516, B:G.516

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, K. et al., Structural snapshots of TRPV1 reveal mechanism of polymodal functionality. Cell (2021)

Release Date

2021-09-22

Peptides

Transient receptor potential cation channel subfamily V member 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Transient receptor potential cation channel subfamily V member 1

Related Entries With Identical Sequence