SMTL ID : 6pqo.1

Cryo-EM structure of the human TRPA1 ion channel in complex with the covalent agonist JT010

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.88 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.748, T.750, I.753, I.762, L.763 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.763 NAG-NAG.2: 5 residues within 4Å: Chain B: N.748, T.750, I.753, I.762, L.763 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.763 NAG-NAG.3: 5 residues within 4Å: Chain C: N.748, T.750, I.753, I.762, L.763 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.763 NAG-NAG.4: 5 residues within 4Å: Chain D: N.748, T.750, I.753, I.762, L.763 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.763

4 x JT0: 2-chloro-N-[4-(4-methoxyphenyl)-1,3-thiazol-2-yl]-N-(3-methoxypropyl)acetamide(Covalent)

JT0.5: 9 residues within 4Å: Chain A: L.610, C.622, I.624, K.662, Q.665, C.666, P.667, F.670, T.685 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.624, A:P.667, A:F.670, A:F.670 Hydrogen bonds: A:T.685 JT0.14: 9 residues within 4Å: Chain B: L.610, C.622, I.624, K.662, Q.665, C.666, P.667, F.670, T.685 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.624, B:P.667, B:F.670, B:F.670 Hydrogen bonds: B:T.685 JT0.20: 9 residues within 4Å: Chain C: L.610, C.622, I.624, K.662, Q.665, C.666, P.667, F.670, T.685 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.624, C:P.667, C:F.670, C:F.670 Hydrogen bonds: C:T.685 JT0.28: 9 residues within 4Å: Chain D: L.610, C.622, I.624, K.662, Q.665, C.666, P.667, F.670, T.685 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.624, D:P.667, D:F.670, D:F.670 Hydrogen bonds: D:T.685

8 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.6: 6 residues within 4Å: Chain A: L.709, W.712, F.854, E.855, N.856 Ligands: 6OU.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.855, A:N.856 Salt bridges: A:E.855 pi-Cation interactions: A:W.712 LBN.7: 20 residues within 4Å: Chain A: D.803, I.804, S.805, Y.841, M.845, L.849, Q.852, I.861, L.864, E.865, L.868, K.869, L.872, T.875, F.910 Chain B: L.937, V.943, I.947, F.948 Ligands: 6OU.26 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.804, A:L.864, A:L.868, A:L.872, A:F.910, B:L.937, B:V.943, B:I.947, B:F.948 Hydrogen bonds: A:E.865 Salt bridges: A:D.803, A:K.869, A:K.869 LBN.15: 7 residues within 4Å: Chain B: L.709, W.712, F.854, E.855, N.856 Chain C: F.880 Ligands: 6OU.19 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.880 Hydrogen bonds: B:E.855, B:N.856 Salt bridges: B:E.855 pi-Cation interactions: B:W.712 LBN.16: 21 residues within 4Å: Chain B: D.803, I.804, S.805, Y.841, M.845, L.849, Q.852, I.861, L.864, E.865, L.868, K.869, L.872, T.875, F.910 Chain C: L.937, A.940, S.944, I.947, F.948 Ligands: 6OU.11 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:I.804, B:L.864, B:L.868, B:L.872, B:F.910, C:L.937, C:A.940, C:I.947, C:I.947 Hydrogen bonds: B:E.865 Salt bridges: B:D.803, B:K.869, B:K.869 LBN.21: 7 residues within 4Å: Chain C: L.709, W.712, F.854, E.855, N.856 Chain D: F.880 Ligands: 6OU.27 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.855, C:N.856 Salt bridges: C:E.855 pi-Cation interactions: C:W.712 Hydrophobic interactions: D:F.880 LBN.22: 20 residues within 4Å: Chain C: D.803, I.804, S.805, Y.841, M.845, L.849, Q.852, I.861, L.864, E.865, L.868, K.869, L.872, T.875, F.910 Chain D: A.940, S.944, I.947, F.948 Ligands: 6OU.18 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.804, C:L.864, C:L.868, C:L.872, C:F.910, D:A.940, D:I.947, D:I.947, D:F.948 Hydrogen bonds: C:E.865 Salt bridges: C:D.803, C:K.869, C:K.869 LBN.29: 7 residues within 4Å: Chain A: F.880 Chain D: L.709, W.712, F.854, E.855, N.856 Ligands: 6OU.12 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:F.880 Hydrogen bonds: D:E.855, D:N.856 Salt bridges: D:E.855 pi-Cation interactions: D:W.712 LBN.30: 21 residues within 4Å: Chain A: L.937, A.940, S.944, I.947, F.948 Chain D: D.803, I.804, S.805, Y.841, M.845, L.849, Q.852, I.861, L.864, E.865, L.868, K.869, L.872, T.875, F.910 Ligands: 6OU.25 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain D Hydrophobic interactions: A:L.937, A:A.940, A:I.947, D:I.804, D:L.864, D:L.868, D:L.872, D:F.910 Hydrogen bonds: D:E.865 Salt bridges: D:D.803, D:K.869, D:K.869

16 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.8: 11 residues within 4Å: Chain A: Y.927, V.936, F.939, V.943, I.947, F.948 Chain D: S.901, L.903, I.907 Ligands: 6OU.25, 6OU.27 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:I.947, A:F.948, D:I.907 Hydrogen bonds: A:Y.927, D:S.901, D:S.901 6OU.9: 6 residues within 4Å: Chain A: I.732, T.735, I.736, V.739, N.740 Ligands: 6OU.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.732, A:I.736 6OU.10: 12 residues within 4Å: Chain A: S.901, L.903, L.904, I.907 Chain B: Y.927, V.936, F.939, V.943, I.947, F.948 Ligands: 6OU.12, 6OU.26 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.903, A:I.907, B:I.947, B:F.948 Hydrogen bonds: A:S.901, B:Y.927 6OU.11: 7 residues within 4Å: Chain A: C.1026 Chain B: K.869, L.872, R.873, T.875 Ligands: LBN.16, 6OU.23 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.872, B:T.875 Salt bridges: B:K.869, B:K.869, B:R.873 6OU.12: 7 residues within 4Å: Chain A: I.879, L.883, P.902, L.903 Ligands: 6OU.10, LBN.29, 6OU.32 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.879, A:L.903 6OU.13: 6 residues within 4Å: Chain B: I.879, L.883, P.902 Ligands: LBN.6, 6OU.9, 6OU.23 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.879, B:L.883 6OU.17: 6 residues within 4Å: Chain B: I.732, T.735, I.736, V.739, N.740 Ligands: 6OU.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.732, B:I.736 6OU.18: 7 residues within 4Å: Chain B: C.1026 Chain C: K.869, L.872, R.873, T.875 Ligands: LBN.22, 6OU.31 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.872, C:T.875 Salt bridges: C:K.869, C:K.869, C:R.873 6OU.19: 6 residues within 4Å: Chain C: I.879, L.883, P.902 Ligands: LBN.15, 6OU.17, 6OU.31 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.879 6OU.23: 11 residues within 4Å: Chain B: S.901, L.903, I.907 Chain C: Y.927, V.936, F.939, V.943, I.947, F.948 Ligands: 6OU.11, 6OU.13 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.907, C:I.947, C:F.948 Hydrogen bonds: B:S.901, B:S.901, C:Y.927 6OU.24: 6 residues within 4Å: Chain C: I.732, T.735, I.736, V.739, N.740 Ligands: 6OU.27 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.732, C:I.736 6OU.25: 7 residues within 4Å: Chain C: C.1026 Chain D: K.869, L.872, R.873, T.875 Ligands: 6OU.8, LBN.30 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.872, D:T.875 Salt bridges: D:K.869, D:K.869, D:R.873 6OU.26: 7 residues within 4Å: Chain A: K.869, L.872, R.873, T.875 Chain D: C.1026 Ligands: LBN.7, 6OU.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.872, A:T.875 Salt bridges: A:K.869, A:K.869, A:R.873 6OU.27: 6 residues within 4Å: Chain D: I.879, L.883, P.902 Ligands: 6OU.8, LBN.21, 6OU.24 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.879 6OU.31: 11 residues within 4Å: Chain C: S.901, L.903, I.907 Chain D: Y.927, V.936, F.939, V.943, I.947, F.948 Ligands: 6OU.18, 6OU.19 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.907, D:I.947, D:F.948 Hydrogen bonds: C:S.901, C:S.901, D:Y.927 6OU.32: 6 residues within 4Å: Chain D: I.732, T.735, I.736, V.739, N.740 Ligands: 6OU.12 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.732, D:I.736

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suo, Y. et al., Structural Insights into Electrophile Irritant Sensing by the Human TRPA1 Channel. Neuron (2020)

Release Date

2020-01-08

Peptides

Transient receptor potential cation channel subfamily A member 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

Membrane

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

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