SMTL ID : 6pqp.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.06 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: 6 residues within 4Å: Chain A: N.748, T.750, I.753, L.763, P.822, L.823 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain B: N.748, T.750, I.753, L.763, P.822, L.823 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain C: N.748, T.750, I.753, L.763, P.822, L.823 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain D: N.748, T.750, I.753, L.763, P.822, L.823 No protein-ligand interaction detected (PLIP)

4 x 9BE: N-benzylthioformamide(Covalent)

9BE.5: 8 residues within 4Å: Chain A: F.613, C.622, P.623, I.624, K.662, Y.663, L.664, Q.665 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.624 9BE.12: 8 residues within 4Å: Chain B: F.613, C.622, P.623, I.624, K.662, Y.663, L.664, Q.665 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.624 9BE.19: 8 residues within 4Å: Chain C: F.613, C.622, P.623, I.624, K.662, Y.663, L.664, Q.665 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.624 9BE.27: 8 residues within 4Å: Chain D: F.613, C.622, P.623, I.624, K.662, Y.663, L.664, Q.665 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.624

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

6OU.6: 5 residues within 4Å: Chain A: I.732, T.735, V.739, N.740 Ligands: 6OU.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.732, A:V.739 6OU.7: 5 residues within 4Å: Chain A: K.869, L.872, R.873, T.875 Ligands: LBN.10 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:K.869 6OU.8: 13 residues within 4Å: Chain A: W.810, I.811, T.814, I.818, H.830, Q.834, C.835, F.842 Chain C: P.935, V.936, L.937 Ligands: LBN.10, 6OU.23 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.810, A:I.811, A:I.818, A:F.842, C:V.936 Hydrogen bonds: A:Q.834, C:V.936 6OU.9: 13 residues within 4Å: Chain A: Y.927, V.936, F.939, V.943, I.947, F.948 Chain B: S.901, L.903, L.904, I.907 Ligands: 6OU.15, LBN.16, 6OU.17 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.939, A:I.947, A:I.947, A:F.948, B:I.907 Hydrogen bonds: A:Y.927, B:S.901 6OU.11: 7 residues within 4Å: Chain A: I.879, L.883, P.902, L.903 Chain B: W.844 Ligands: 6OU.13, 6OU.23 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.844, A:I.879, A:I.879, A:L.883, A:L.903, A:L.903 6OU.13: 5 residues within 4Å: Chain B: I.732, T.735, V.739, N.740 Ligands: 6OU.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.732, B:V.739 6OU.14: 5 residues within 4Å: Chain B: K.869, L.872, R.873, T.875 Ligands: LBN.16 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:K.869 6OU.15: 13 residues within 4Å: Chain A: P.935, V.936, L.937 Chain B: W.810, I.811, T.814, I.818, H.830, Q.834, C.835, F.842 Ligands: 6OU.9, LBN.16 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.936, B:W.810, B:I.811, B:I.818, B:F.842 Hydrogen bonds: A:V.936, B:Q.834 6OU.17: 7 residues within 4Å: Chain B: I.879, L.883, P.902, L.903 Chain D: W.844 Ligands: 6OU.9, 6OU.28 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:I.879, B:I.879, B:L.883, B:L.903, B:L.903, D:W.844 6OU.18: 7 residues within 4Å: Chain A: W.844 Chain C: I.879, L.883, P.902, L.903 Ligands: 6OU.6, 6OU.31 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.879, C:I.879, C:L.883, C:L.903, C:L.903, A:W.844 6OU.20: 5 residues within 4Å: Chain C: I.732, T.735, V.739, N.740 Ligands: 6OU.26 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.732, C:V.739 6OU.21: 5 residues within 4Å: Chain C: K.869, L.872, R.873, T.875 Ligands: LBN.24 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:K.869 6OU.22: 12 residues within 4Å: Chain C: W.810, I.811, T.814, I.818, H.830, Q.834, C.835, F.842 Chain D: P.935, V.936 Ligands: LBN.24, 6OU.31 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:W.810, C:I.811, C:I.818, C:F.842, D:V.936 Hydrogen bonds: C:Q.834, D:V.936 6OU.23: 13 residues within 4Å: Chain A: S.901, L.903, L.904, I.907 Chain C: Y.927, V.936, F.939, V.943, I.947, F.948 Ligands: 6OU.8, LBN.10, 6OU.11 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:I.907, C:F.939, C:I.947, C:I.947, C:F.948 Hydrogen bonds: A:S.901, C:Y.927 6OU.25: 13 residues within 4Å: Chain B: Y.927, V.936, F.939, V.943, I.947, F.948 Chain D: S.901, L.903, L.904, I.907 Ligands: 6OU.26, 6OU.30, LBN.32 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.939, B:I.947, B:I.947, B:F.948, D:I.907 Hydrogen bonds: B:Y.927, D:S.901 6OU.26: 7 residues within 4Å: Chain C: W.844 Chain D: I.879, L.883, P.902, L.903 Ligands: 6OU.20, 6OU.25 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.879, D:I.879, D:L.883, D:L.903, C:W.844 6OU.28: 5 residues within 4Å: Chain D: I.732, T.735, V.739, N.740 Ligands: 6OU.17 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.732, D:V.739 6OU.29: 5 residues within 4Å: Chain D: K.869, L.872, R.873, T.875 Ligands: LBN.32 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:K.869 6OU.30: 13 residues within 4Å: Chain B: P.935, V.936, L.937 Chain D: W.810, I.811, T.814, I.818, H.830, Q.834, C.835, F.842 Ligands: 6OU.25, LBN.32 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:W.810, D:I.811, D:I.818, D:F.842, B:V.936 Hydrogen bonds: D:Q.834, B:V.936 6OU.31: 13 residues within 4Å: Chain C: S.901, L.903, L.904, I.907 Chain D: Y.927, V.936, F.939, V.943, I.947, F.948 Ligands: 6OU.18, 6OU.22, LBN.24 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.939, D:I.947, D:I.947, D:F.948, C:I.907 Hydrogen bonds: D:Y.927, C:S.901

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

LBN.10: 23 residues within 4Å: Chain A: D.803, I.804, S.805, Y.841, F.842, M.845, L.849, Q.852, I.861, L.864, E.865, L.868, K.869, L.871, L.872, T.875 Chain C: A.940, V.943, I.947, F.948 Ligands: 6OU.7, 6OU.8, 6OU.23 17 PLIP interactions: 4 interactions with chain C, 13 interactions with chain A Hydrophobic interactions: C:A.940, C:V.943, C:I.947, C:F.948, A:I.804, A:Y.841, A:F.842, A:L.849, A:L.864, A:L.868, A:L.871, A:L.872 Hydrogen bonds: A:E.865, A:E.865 Salt bridges: A:D.803, A:K.869, A:K.869 LBN.16: 23 residues within 4Å: Chain A: A.940, V.943, I.947, F.948 Chain B: D.803, I.804, S.805, Y.841, F.842, M.845, L.849, Q.852, I.861, L.864, E.865, L.868, K.869, L.871, L.872, T.875 Ligands: 6OU.9, 6OU.14, 6OU.15 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.804, B:Y.841, B:F.842, B:L.849, B:L.864, B:L.868, B:L.871, B:L.872, A:A.940, A:V.943, A:I.947, A:F.948 Hydrogen bonds: B:E.865, B:E.865 Salt bridges: B:D.803, B:K.869, B:K.869 LBN.24: 22 residues within 4Å: Chain C: D.803, I.804, S.805, Y.841, F.842, M.845, L.849, Q.852, I.861, L.864, E.865, L.868, K.869, L.871, L.872, T.875 Chain D: A.940, I.947, F.948 Ligands: 6OU.21, 6OU.22, 6OU.31 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.804, C:Y.841, C:F.842, C:L.849, C:L.864, C:L.868, C:L.871, C:L.872, D:A.940, D:I.947, D:F.948 Hydrogen bonds: C:E.865, C:E.865 Salt bridges: C:D.803, C:K.869, C:K.869 LBN.32: 22 residues within 4Å: Chain B: V.943, I.947, F.948 Chain D: D.803, I.804, S.805, Y.841, F.842, M.845, L.849, Q.852, I.861, L.864, E.865, L.868, K.869, L.871, L.872, T.875 Ligands: 6OU.25, 6OU.29, 6OU.30 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:I.804, D:Y.841, D:F.842, D:L.849, D:L.864, D:L.868, D:L.871, D:L.872, B:V.943, B:I.947, B:F.948 Hydrogen bonds: D:E.865, D:E.865 Salt bridges: D:D.803, D:K.869, D:K.869

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
D

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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