SMTL ID : 9kdc.1

Structure of hTRPC3 in complex with Nb3-37 at 3.01 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

2 x ZN: ZINC ION(Non-functional Binders)

ZN.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

12 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: E.158, D.883 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.158, A:E.158, A:D.883 CA.3: 4 residues within 4Å: Chain A: E.871, N.873, E.876 Chain B: E.874 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.871, A:E.876 CA.4: 4 residues within 4Å: Chain A: E.525, E.528, N.543, D.546 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.525 CA.6: 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.7: 6 residues within 4Å: Chain B: K.867, D.870, E.871, N.873, E.876 Chain C: E.874 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.871, B:E.876 CA.8: 4 residues within 4Å: Chain B: E.525, E.528, N.543, D.546 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.525 CA.10: 2 residues within 4Å: Chain C: E.158, D.883 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.158, C:E.158, C:D.883 CA.11: 4 residues within 4Å: Chain C: E.871, N.873, E.876 Chain D: E.874 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.871, C:E.876 CA.12: 4 residues within 4Å: Chain C: E.525, E.528, N.543, D.546 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.525 CA.15: 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.16: 6 residues within 4Å: Chain A: E.874 Chain D: K.867, D.870, E.871, N.873, E.876 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.871 CA.17: 4 residues within 4Å: Chain D: E.525, E.528, N.543, D.546 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.525

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

01.5: 14 residues within 4Å: Chain A: L.643, E.688, F.691, K.692, F.695, W.696 Chain B: V.660, N.718, Y.721, V.722, G.725, I.726, V.729, T.730 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.660, B:V.722, B:V.722, B:I.726, B:I.726, B:V.729, B:V.729, B:T.730, A:L.643, A:F.691, A:F.695 Hydrogen bonds: A:E.688 01.9: 14 residues within 4Å: Chain B: L.643, M.654, F.691, K.692, F.695, W.696 Chain C: V.660, N.718, Y.721, V.722, G.725, I.726, V.729, T.730 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:V.660, C:V.722, C:V.722, C:I.726, C:I.726, C:V.729, C:V.729, C:T.730, B:L.643, B:F.691, B:F.695, B:F.695, B:F.695 01.13: 14 residues within 4Å: Chain C: L.643, E.688, F.691, K.692, F.695, W.696 Chain D: V.660, N.718, Y.721, V.722, G.725, I.726, V.729, T.730 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:L.643, C:F.691, C:F.691, C:F.695, D:V.660, D:V.722, D:V.722, D:I.726, D:I.726, D:V.729, D:V.729, D:T.730 Hydrogen bonds: C:E.688 01.18: 15 residues within 4Å: Chain A: V.660, N.718, Y.721, V.722, G.725, I.726, V.729, T.730 Chain D: L.643, M.654, E.688, F.691, K.692, F.695, W.696 17 PLIP interactions: 9 interactions with chain D, 8 interactions with chain A Hydrophobic interactions: D:L.643, D:F.691, D:F.691, D:F.695, D:F.695, D:F.695, D:W.696, A:V.660, A:V.722, A:V.722, A:I.726, A:I.726, A:V.729, A:V.729, A:T.730 Hydrogen bonds: D:E.688, D:E.688

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

Short transient receptor potential channel 3: ABCD
Nb3-37: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Short transient receptor potential channel 3

Nb3-37

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