SMTL ID : 8hk7.1

Structure of PKD2-F604P (Polycystin-2, TRPP2) with ML-SA1

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: 3 residues within 4Å: Chain A: N.180, K.194, E.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.180 NAG.2: 3 residues within 4Å: Chain A: P.212, N.214, N.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.264 NAG.3: 3 residues within 4Å: Chain A: D.225, N.227, N.399 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.225, A:N.227 NAG.6: 3 residues within 4Å: Chain B: N.180, K.194, E.195 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.180 NAG.7: 3 residues within 4Å: Chain B: P.212, N.214, N.264 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.264 NAG.8: 3 residues within 4Å: Chain B: D.225, N.227, N.399 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.225, B:N.227 NAG.10: 3 residues within 4Å: Chain C: N.180, K.194, E.195 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.180 NAG.11: 3 residues within 4Å: Chain C: P.212, N.214, N.264 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.264 NAG.12: 3 residues within 4Å: Chain C: D.225, N.227, N.399 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.225, C:N.227 NAG.14: 3 residues within 4Å: Chain D: N.180, K.194, E.195 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.180 NAG.15: 3 residues within 4Å: Chain D: P.212, N.214, N.264 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.264 NAG.16: 3 residues within 4Å: Chain D: D.225, N.227, N.399 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.225, D:N.227

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: L.493 Chain B: L.493 Chain C: L.493 Chain D: L.493 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C Metal complexes: A:L.493, B:L.493, D:L.493, C:L.493

4 x AQV: 2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]ethyl}-1H-isoindole-1,3(2H)-dione(Non-covalent)

AQV.5: 12 residues within 4Å: Chain A: E.503, A.504, N.505, R.506, V.507 Chain B: H.231, W.232, Q.308, Y.405, I.408, Q.409, N.412 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.412 Hydrophobic interactions: A:R.506 AQV.9: 12 residues within 4Å: Chain B: E.503, A.504, N.505, R.506, V.507 Chain C: H.231, W.232, Q.308, Y.405, I.408, Q.409, N.412 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.412 Hydrophobic interactions: B:R.506 AQV.13: 12 residues within 4Å: Chain C: E.503, A.504, N.505, R.506, V.507 Chain D: H.231, W.232, Q.308, Y.405, I.408, Q.409, N.412 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.412 Hydrophobic interactions: C:R.506 AQV.17: 12 residues within 4Å: Chain A: H.231, W.232, Q.308, Y.405, I.408, Q.409, N.412 Chain D: E.503, A.504, N.505, R.506, V.507 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:R.506 Hydrogen bonds: A:N.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Molecular and structural basis of the dual regulation of the polycystin-2 ion channel by small-molecule ligands. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-03-27

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

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