SMTL ID : 7d7f.1

Structure of PKD1L3-CTD/PKD2L1 in calcium-bound state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

hetero-3-1-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.152 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.152 NAG.2: 3 residues within 4Å: Chain A: N.182, N.197, L.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.182 NAG.3: 1 residues within 4Å: Chain A: N.216 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain B: N.152 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain B: N.182, L.196, N.197 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.197 NAG.7: 1 residues within 4Å: Chain B: N.216 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.216 NAG.10: 2 residues within 4Å: Chain C: N.182, N.197 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.182, C:N.197 NAG.11: 1 residues within 4Å: Chain C: N.216 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain D: G.221, N.223, D.368 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.368 NAG.15: 1 residues within 4Å: Chain D: N.113 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.113

5 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.345, E.348, N.362, D.365 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.345 CA.8: 4 residues within 4Å: Chain B: E.345, E.348, N.362, D.365 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.345, B:E.348, B:D.365 CA.9: 5 residues within 4Å: Chain C: E.345, E.348, N.362, D.365, K.430 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.345 CA.12: 1 residues within 4Å: Chain C: L.496 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:L.496 CA.13: 2 residues within 4Å: Chain C: L.92, M.96 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, Q. et al., Structural basis for Ca 2+ activation of the heteromeric PKD1L3/PKD2L1 channel. Nat Commun (2021)

Release Date

2021-09-01

Peptides

Polycystic kidney disease 2-like 1 protein: ABC
Polycystic kidney disease protein 1-like 3: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
A

Membrane

We predict this structure to be a membrane protein.
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Polycystic kidney disease 2-like 1 protein

Polycystic kidney disease protein 1-like 3

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