SMTL ID : 5t4d.1

Cryo-EM structure of Polycystic Kidney Disease protein 2 (PKD2), residues 198-703

Coordinates

PDB Format

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.136, K.150, E.151, Y.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.136, A:E.151 NAG.2: 1 residues within 4Å: Chain A: N.170 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.170 NAG.3: 5 residues within 4Å: Chain A: R.128, D.181, L.182, N.183, Q.345 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.128, A:D.181, A:Q.345 NAG.4: 4 residues within 4Å: Chain B: N.136, K.150, E.151, Y.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.136, B:E.151 NAG.5: 1 residues within 4Å: Chain B: N.170 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.170 NAG.6: 5 residues within 4Å: Chain B: R.128, D.181, L.182, N.183, Q.345 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.128, B:D.181, B:Q.345 NAG.7: 4 residues within 4Å: Chain C: N.136, K.150, E.151, Y.153 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.136, C:E.151 NAG.8: 1 residues within 4Å: Chain C: N.170 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.170 NAG.9: 5 residues within 4Å: Chain C: R.128, D.181, L.182, N.183, Q.345 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.128, C:D.181, C:Q.345 NAG.10: 4 residues within 4Å: Chain D: N.136, K.150, E.151, Y.153 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.136, D:E.151 NAG.11: 1 residues within 4Å: Chain D: N.170 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:N.170 NAG.12: 5 residues within 4Å: Chain D: R.128, D.181, L.182, N.183, Q.345 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.128, D:D.181, D:Q.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, P.S. et al., The Structure of the Polycystic Kidney Disease Channel PKD2 in Lipid Nanodiscs. Cell (2016)

Release Date

2016-11-02

Peptides

hPKD:198-703, 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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hPKD:198-703, Polycystin-2