SMTL ID : 6pqq.1

Cryo-EM structure of human TRPA1 C621S mutant in the apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.81 Å

Oligo State

homo-tetramer

Ligands

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

LBN.1: 10 residues within 4Å: Chain A: L.709, W.712, C.728, F.847, F.854, E.855, N.856, C.857, L.1024 Chain B: F.880 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.847, A:L.1024, B:F.880 Hydrogen bonds: A:E.855, A:E.855, A:N.856 Salt bridges: A:E.855 pi-Cation interactions: A:W.712, A:W.712 LBN.2: 24 residues within 4Å: Chain A: D.803, I.804, S.805, Y.841, M.845, Q.852, I.861, L.864, E.865, L.868, K.869, L.871, L.872, T.875, I.879 Chain B: L.937, A.940, V.943, S.944, I.947, F.948 Ligands: 6OU.3, 6OU.4, 6OU.13 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.804, A:I.861, A:L.864, A:L.868, A:L.868, A:L.871, A:L.872, A:I.879, B:L.937, B:A.940, B:V.943, B:I.947, B:F.948 Hydrogen bonds: A:E.865, A:E.865 Salt bridges: A:D.803, A:K.869, A:K.869 LBN.8: 9 residues within 4Å: Chain B: L.709, W.712, C.728, F.847, F.854, E.855, N.856, C.857, L.1024 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.847, B:L.1024 Hydrogen bonds: B:E.855, B:E.855, B:N.856 Salt bridges: B:E.855 pi-Cation interactions: B:W.712, B:W.712 LBN.9: 22 residues within 4Å: Chain B: D.803, I.804, S.805, Y.841, M.845, Q.852, I.861, L.864, E.865, L.868, K.869, L.871, L.872, T.875, I.879 Chain D: V.943, S.944, I.947, F.948 Ligands: 6OU.10, 6OU.11, 6OU.27 17 PLIP interactions: 4 interactions with chain D, 13 interactions with chain B Hydrophobic interactions: D:V.943, D:I.947, D:F.948, D:F.948, B:I.804, B:I.861, B:L.864, B:L.868, B:L.868, B:L.871, B:L.872, B:I.879 Hydrogen bonds: B:E.865, B:E.865 Salt bridges: B:D.803, B:K.869, B:K.869 LBN.15: 9 residues within 4Å: Chain C: L.709, W.712, C.728, F.847, F.854, E.855, N.856, C.857, L.1024 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.847, C:L.1024 Hydrogen bonds: C:E.855, C:E.855, C:N.856 Salt bridges: C:E.855 pi-Cation interactions: C:W.712, C:W.712 LBN.16: 22 residues within 4Å: Chain A: L.937, V.943, S.944, I.947, F.948 Chain C: D.803, I.804, S.805, Y.841, M.845, Q.852, I.861, L.864, E.865, L.868, K.869, L.871, L.872, T.875, I.879 Ligands: 6OU.17, 6OU.18 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:I.804, C:I.861, C:L.864, C:L.868, C:L.868, C:L.871, C:L.872, C:I.879, A:L.937, A:V.943, A:I.947, A:F.948 Hydrogen bonds: C:E.865, C:E.865 Salt bridges: C:D.803, C:K.869, C:K.869 LBN.22: 11 residues within 4Å: Chain C: F.880 Chain D: L.709, W.712, C.728, F.847, F.854, E.855, N.856, C.857, L.1024 Ligands: 6OU.19 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.847, D:L.1024 Hydrogen bonds: D:E.855, D:E.855, D:N.856 Salt bridges: D:E.855 pi-Cation interactions: D:W.712, D:W.712 LBN.23: 23 residues within 4Å: Chain C: L.937, A.940, S.944, I.947, F.948 Chain D: D.803, I.804, S.805, Y.841, M.845, Q.852, I.861, L.864, E.865, L.868, K.869, L.871, L.872, T.875, I.879 Ligands: 6OU.20, 6OU.24, 6OU.25 17 PLIP interactions: 4 interactions with chain C, 13 interactions with chain D Hydrophobic interactions: C:L.937, C:A.940, C:I.947, C:F.948, D:I.804, D:I.861, D:L.864, D:L.868, D:L.868, D:L.871, D:L.872, D:I.879 Hydrogen bonds: D:E.865, D:E.865 Salt bridges: D:D.803, D:K.869, D:K.869

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

6OU.3: 4 residues within 4Å: Chain A: L.872, T.875 Chain C: C.1026 Ligands: LBN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.872, A:L.872, A:T.875 Salt bridges: A:K.869, A:R.873 6OU.4: 9 residues within 4Å: Chain A: I.804, W.810, T.814, T.815, H.830, Q.834 Chain B: P.935 Ligands: LBN.2, 6OU.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.804, A:W.810 Hydrogen bonds: A:Q.834 Salt bridges: A:H.830 6OU.5: 6 residues within 4Å: Chain A: I.879, L.883, P.902, L.903 Ligands: 6OU.13, 6OU.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.879, A:L.883, A:L.883, A:L.903 6OU.6: 10 residues within 4Å: Chain A: Y.927, V.936, F.939, V.943, F.948 Chain C: S.901, L.903, I.907 Ligands: 6OU.18, 6OU.19 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.939, A:V.943, A:F.948, C:L.903, C:I.907 Hydrogen bonds: C:S.901, C:S.901 6OU.7: 8 residues within 4Å: Chain A: I.732, T.735, I.736, V.739, N.740, N.767, L.770 Ligands: 6OU.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.732, A:I.732, A:I.736, A:I.736, A:V.739 Hydrogen bonds: A:N.740, A:N.767 6OU.10: 4 residues within 4Å: Chain A: C.1026 Chain B: L.872, T.875 Ligands: LBN.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.872, B:L.872, B:T.875 Salt bridges: B:K.869, B:R.873 6OU.11: 10 residues within 4Å: Chain B: I.804, W.810, T.814, T.815, H.830, Q.834 Chain D: P.935, V.936 Ligands: LBN.9, 6OU.27 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.804, B:W.810 Hydrogen bonds: B:Q.834 Salt bridges: B:H.830 6OU.12: 6 residues within 4Å: Chain B: I.879, L.883, P.902, L.903 Ligands: 6OU.7, 6OU.27 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.879, B:L.883, B:L.883, B:L.903 6OU.13: 10 residues within 4Å: Chain A: S.901, L.903 Chain B: Y.927, V.936, F.939, V.943, F.948 Ligands: LBN.2, 6OU.4, 6OU.5 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.901, A:S.901 Hydrophobic interactions: B:F.939, B:V.943, B:F.948 6OU.14: 8 residues within 4Å: Chain B: I.732, T.735, I.736, V.739, N.740, N.767, L.770 Ligands: 6OU.26 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.732, B:I.732, B:I.736, B:I.736, B:V.739 Hydrogen bonds: B:N.740, B:N.767 6OU.17: 4 residues within 4Å: Chain C: L.872, T.875 Chain D: C.1026 Ligands: LBN.16 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.872, C:L.872, C:T.875 Salt bridges: C:K.869, C:R.873 6OU.18: 8 residues within 4Å: Chain C: I.804, W.810, T.814, T.815, H.830, Q.834 Ligands: 6OU.6, LBN.16 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.804, C:W.810 Hydrogen bonds: C:Q.834 Salt bridges: C:H.830 6OU.19: 7 residues within 4Å: Chain C: I.879, L.883, P.902, L.903 Ligands: 6OU.6, LBN.22, 6OU.28 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.879, C:L.883, C:L.883, C:L.903 6OU.20: 10 residues within 4Å: Chain C: Y.927, V.936, F.939, V.943, F.948 Chain D: S.901, L.903 Ligands: LBN.23, 6OU.25, 6OU.26 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.939, C:V.943, C:F.948 Hydrogen bonds: D:S.901, D:S.901 6OU.21: 8 residues within 4Å: Chain C: I.732, T.735, I.736, V.739, N.740, N.767, L.770 Ligands: 6OU.5 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.732, C:I.732, C:I.736, C:I.736, C:V.739 Hydrogen bonds: C:N.740, C:N.767 6OU.24: 4 residues within 4Å: Chain B: C.1026 Chain D: L.872, T.875 Ligands: LBN.23 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.872, D:L.872, D:T.875 Salt bridges: D:K.869, D:R.873 6OU.25: 10 residues within 4Å: Chain C: P.935, V.936 Chain D: I.804, W.810, T.814, T.815, H.830, Q.834 Ligands: 6OU.20, LBN.23 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:V.936, D:I.804, D:W.810 Hydrogen bonds: D:Q.834 Salt bridges: D:H.830 6OU.26: 6 residues within 4Å: Chain D: I.879, L.883, P.902, L.903 Ligands: 6OU.14, 6OU.20 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.879, D:L.883, D:L.883, D:L.903 6OU.27: 10 residues within 4Å: Chain B: S.901, L.903 Chain D: Y.927, V.936, F.939, V.943, F.948 Ligands: LBN.9, 6OU.11, 6OU.12 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:L.903, D:F.939, D:V.943, D:F.948 Hydrogen bonds: B:S.901, B:S.901 6OU.28: 8 residues within 4Å: Chain D: I.732, T.735, I.736, V.739, N.740, N.767, L.770 Ligands: 6OU.19 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.732, D:I.732, D:I.736, D:I.736, D:V.739 Hydrogen bonds: D:N.740, D:N.767

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
A

B
B

C
D

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