SMTL ID : 7or0.1

Cryo-EM structure of the human TRPA1 ion channel in complex with the antagonist 3-60, conformation 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

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.747, S.748, T.749, I.752, E.760 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: N.747, S.748, T.749, I.752, E.760 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain C: N.747, S.748, T.749, I.752, E.760 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: N.747, T.749, I.752, E.760 No protein-ligand interaction detected (PLIP)

4 x 0IG: ~{N}-[4-[4-[(azanylidene-$l^{4}-azanylidene)amino]phenyl]-1,3-thiazol-2-yl]-2-[1,3-dimethyl-2,6-bis(oxidanylidene)purin-7-yl]ethanamide(Non-covalent)

0IG.5: 11 residues within 4Å: Chain A: L.707, W.711, F.716, M.720, L.850, R.852, F.853, E.854, N.855, Q.979, H.983 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.711, A:E.854, A:N.855 pi-Stacking: A:W.711, A:W.711, A:W.711, A:F.853 0IG.11: 11 residues within 4Å: Chain B: L.707, W.711, F.716, M.720, L.850, R.852, F.853, E.854, N.855, Q.979, H.983 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.711, B:E.854, B:N.855 pi-Stacking: B:W.711, B:W.711, B:W.711, B:F.853 0IG.18: 11 residues within 4Å: Chain C: L.707, W.711, F.716, M.720, L.850, R.852, F.853, E.854, N.855, Q.979, H.983 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:W.711, C:E.854, C:N.855 pi-Stacking: C:W.711, C:W.711, C:W.711, C:F.853 0IG.25: 11 residues within 4Å: Chain D: L.707, W.711, F.716, M.720, L.850, R.852, F.853, E.854, N.855, Q.979, H.983 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:W.711, D:E.854, D:N.855 pi-Stacking: D:W.711, D:W.711, D:W.711, D:F.853

8 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.6: 11 residues within 4Å: Chain A: I.803, A.836, Y.840, M.844, L.863, E.864, L.867, K.868, L.871 Chain B: Q.940 Ligands: PC1.13 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.940, A:I.803, A:L.867 Hydrogen bonds: A:Q.851 Salt bridges: A:K.868 PC1.7: 6 residues within 4Å: Chain A: Y.926, F.938, I.946, F.947 Chain D: L.902 Ligands: PC1.26 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.938, A:I.946, A:F.947 Hydrogen bonds: A:Y.926 PC1.12: 13 residues within 4Å: Chain B: I.803, A.836, Y.840, M.844, L.863, E.864, L.867, K.868, L.871 Chain C: L.936, A.939, Q.940 Ligands: PC1.20 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.803, B:L.867, C:L.936, C:A.939, C:Q.940 Hydrogen bonds: B:Q.851 Salt bridges: B:K.868 PC1.13: 6 residues within 4Å: Chain A: L.902 Chain B: Y.926, F.938, I.946, F.947 Ligands: PC1.6 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.938, B:I.946, B:F.947, A:L.902 Hydrogen bonds: B:Y.926 PC1.19: 13 residues within 4Å: Chain C: I.803, A.836, Y.840, M.844, L.863, E.864, L.867, K.868, L.871 Chain D: L.936, A.939, Q.940 Ligands: PC1.27 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.803, C:L.867, D:L.936, D:A.939, D:Q.940 Hydrogen bonds: C:Q.851 Salt bridges: C:K.868 PC1.20: 7 residues within 4Å: Chain B: L.902, I.906 Chain C: Y.926, F.938, I.946, F.947 Ligands: PC1.12 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:I.906, C:F.938, C:I.946, C:F.947 Hydrogen bonds: C:Y.926 PC1.26: 11 residues within 4Å: Chain A: Q.940 Chain D: I.803, A.836, Y.840, M.844, L.863, E.864, L.867, K.868, L.871 Ligands: PC1.7 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.803, D:L.867, A:Q.940 Hydrogen bonds: D:Q.851 Salt bridges: D:K.868 PC1.27: 6 residues within 4Å: Chain C: L.902 Chain D: Y.926, F.938, I.946, F.947 Ligands: PC1.19 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.938, D:I.946, D:F.947, C:L.902 Hydrogen bonds: D:Y.926

5 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.8: 4 residues within 4Å: Chain A: E.788, Q.791, N.805, E.808 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.788 CA.14: 4 residues within 4Å: Chain B: E.788, Q.791, N.805, E.808 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.788 CA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.21: 4 residues within 4Å: Chain C: E.788, Q.791, N.805, E.808 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.788 CA.28: 4 residues within 4Å: Chain D: E.788, Q.791, N.805, E.808 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.788

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

NAG.9: 3 residues within 4Å: Chain A: N.753, E.754, I.761 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.761 NAG.15: 3 residues within 4Å: Chain B: N.753, E.754, I.761 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.761 NAG.22: 3 residues within 4Å: Chain C: N.753, E.754, I.761 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.761 NAG.29: 3 residues within 4Å: Chain D: N.753, E.754, I.761 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.761

4 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.10: 5 residues within 4Å: Chain A: K.593, K.1046 Chain B: K.1048, Y.1049, K.1052 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.1049 Salt bridges: B:K.1048, B:K.1052, A:K.593, A:K.1046 IHP.16: 5 residues within 4Å: Chain B: K.593, K.1046 Chain C: K.1048, Y.1049, K.1052 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Y.1049 Salt bridges: C:K.1048, C:K.1052, B:K.593, B:K.593, B:K.1046 IHP.23: 5 residues within 4Å: Chain C: K.593, K.1046 Chain D: K.1048, Y.1049, K.1052 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Salt bridges: C:K.593, C:K.1046, D:K.1048, D:K.1052 Hydrogen bonds: D:Y.1049 IHP.24: 5 residues within 4Å: Chain A: K.1048, Y.1049, K.1052 Chain D: K.593, K.1046 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:Y.1049 Salt bridges: A:K.1048, A:K.1052, D:K.593, D:K.593, D:K.1046

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grieben, M. et al., Cryo-EM structure of the human TRPA1 ion channel in complex with the antagonist 3-60. To Be Published

Release Date

2022-06-22

Peptides

Transient receptor potential cation channel subfamily A member 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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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