SMTL ID : 6wb8.1

Cryo-EM structure of PKD2 C331S disease variant

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.292, S.294, E.307, Y.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.307 NAG.2: 1 residues within 4Å: Chain A: N.326 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.326 NAG.3: 4 residues within 4Å: Chain A: D.337, L.338, N.339, Q.501 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.337, A:N.339, A:Q.501 NAG.4: 4 residues within 4Å: Chain B: N.292, S.294, E.307, Y.309 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.307 NAG.5: 1 residues within 4Å: Chain B: N.326 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.326 NAG.6: 4 residues within 4Å: Chain B: D.337, L.338, N.339, Q.501 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.337, B:N.339, B:Q.501 NAG.7: 4 residues within 4Å: Chain C: N.292, S.294, E.307, Y.309 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.307 NAG.8: 1 residues within 4Å: Chain C: N.326 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.326 NAG.9: 4 residues within 4Å: Chain C: D.337, L.338, N.339, Q.501 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.337, C:N.339, C:Q.501 NAG.10: 4 residues within 4Å: Chain D: N.292, S.294, E.307, Y.309 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.307 NAG.11: 1 residues within 4Å: Chain D: N.326 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:N.326 NAG.12: 4 residues within 4Å: Chain D: D.337, L.338, N.339, Q.501 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.337, D:N.339, D:Q.501

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vien, T.N. et al., Molecular dysregulation of ciliary polycystin-2 channels caused by variants in the TOP domain. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-04-22

Peptides

Polycystin-2: 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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Polycystin-2