SMTL ID : 9kdb.1

Structure of hTRPC3 in complex with Nb1-25 at 2.67 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: H.263, C.267, C.269, C.272 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.263, B:C.267, B:C.269, B:C.272 ZN.7: 4 residues within 4Å: Chain D: H.263, C.267, C.269, C.272 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.263, D:C.267, D:C.269, D:C.272 ZN.12: 4 residues within 4Å: Chain F: H.263, C.267, C.269, C.272 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.263, F:C.267, F:C.269, F:C.272 ZN.17: 4 residues within 4Å: Chain H: H.263, C.267, C.269, C.272 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.263, H:C.267, H:C.269, H:C.272

12 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain B: E.158, D.883 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.158, B:E.158, B:D.883 CA.3: 4 residues within 4Å: Chain B: E.871, N.873, E.876 Chain H: E.874 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain H Metal complexes: B:E.871, B:E.876, H:E.874 CA.4: 4 residues within 4Å: Chain B: E.525, E.528, N.543, D.546 No protein-ligand interaction detected (PLIP) CA.8: 2 residues within 4Å: Chain D: E.158, D.883 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.158, D:E.158, D:D.883 CA.9: 4 residues within 4Å: Chain B: E.874 Chain D: E.871, N.873, E.876 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Metal complexes: D:E.871, D:E.876, B:E.874 CA.10: 4 residues within 4Å: Chain D: E.525, E.528, N.543, D.546 No protein-ligand interaction detected (PLIP) CA.13: 2 residues within 4Å: Chain F: E.158, D.883 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.158, F:E.158, F:D.883 CA.14: 4 residues within 4Å: Chain D: E.874 Chain F: E.871, N.873, E.876 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain F Metal complexes: D:E.874, F:E.871, F:E.876 CA.15: 4 residues within 4Å: Chain F: E.525, E.528, N.543, D.546 No protein-ligand interaction detected (PLIP) CA.18: 2 residues within 4Å: Chain H: E.158, D.883 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.158, H:E.158, H:D.883 CA.19: 4 residues within 4Å: Chain F: E.874 Chain H: E.871, N.873, E.876 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain F Metal complexes: H:E.871, H:E.876, F:E.874 CA.20: 4 residues within 4Å: Chain H: E.525, E.528, N.543, D.546 No protein-ligand interaction detected (PLIP)

4 x 01: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate

01.5: 13 residues within 4Å: Chain B: L.643, E.688, F.691, K.692, F.695, W.696 Chain H: V.660, N.718, Y.721, V.722, I.726, V.729, T.730 12 PLIP interactions: 5 interactions with chain H, 7 interactions with chain B Hydrophobic interactions: H:V.660, H:V.722, H:I.726, H:V.729, H:T.730, B:L.643, B:F.691, B:F.695 Hydrogen bonds: B:E.688, B:E.688, B:K.692 Salt bridges: B:K.692 01.6: 13 residues within 4Å: Chain B: V.660, N.718, Y.721, V.722, I.726, V.729, T.730 Chain D: L.643, E.688, F.691, K.692, F.695, W.696 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:V.660, B:V.722, B:I.726, B:V.729, B:T.730, D:L.643, D:F.691, D:F.695 Hydrogen bonds: D:E.688, D:E.688, D:K.692 Salt bridges: D:K.692 01.11: 13 residues within 4Å: Chain D: V.660, N.718, Y.721, V.722, I.726, V.729, T.730 Chain F: L.643, E.688, F.691, K.692, F.695, W.696 12 PLIP interactions: 7 interactions with chain F, 5 interactions with chain D Hydrophobic interactions: F:L.643, F:F.691, F:F.695, D:V.660, D:V.722, D:I.726, D:V.729, D:T.730 Hydrogen bonds: F:E.688, F:E.688, F:K.692 Salt bridges: F:K.692 01.16: 13 residues within 4Å: Chain F: V.660, N.718, Y.721, V.722, I.726, V.729, T.730 Chain H: L.643, E.688, F.691, K.692, F.695, W.696 12 PLIP interactions: 5 interactions with chain F, 7 interactions with chain H Hydrophobic interactions: F:V.660, F:V.722, F:I.726, F:V.729, F:T.730, H:L.643, H:F.691, H:F.695 Hydrogen bonds: H:E.688, H:E.688, H:K.692 Salt bridges: H:K.692

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Structural mechanism of the agonist binding on human TRPC3 channel. Nat Commun (2025)

Release Date

2025-10-08

Peptides

Nb1-25: ACEG
Short transient receptor potential channel 3: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
F

E
G

G
H

B
A

D
B

F
C

H
D

Membrane

We predict this structure to be a membrane protein.
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Nb1-25

Short transient receptor potential channel 3

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