SMTL ID : 8k3s.1

Structure of PKD2-F604P complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)(Covalent)

PEF.1: 23 residues within 4Å: Chain A: S.229, S.230, H.231, W.232, G.233, R.292, L.294, S.306, W.307, Q.308, H.402, Y.405, Q.409, N.412, I.413, V.416, F.420 Chain D: E.503, A.504, N.505, R.506, V.507, L.508 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:W.232, A:W.232 Hydrogen bonds: A:R.292, A:R.292, A:R.292, A:S.306, D:E.503 Salt bridges: A:R.292, D:R.506 PEF.6: 20 residues within 4Å: Chain A: E.503, R.506, V.507, L.508 Chain B: S.229, S.230, H.231, W.232, G.233, R.292, L.294, S.306, Q.308, H.402, Y.405, Q.409, N.412, I.413, V.416, F.420 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:E.503, B:R.292, B:R.292 Hydrophobic interactions: B:W.232, B:W.232 Salt bridges: B:R.292 PEF.10: 21 residues within 4Å: Chain B: E.503, R.506, V.507, L.508 Chain C: S.229, S.230, H.231, W.232, G.233, R.292, S.306, W.307, Q.308, H.402, Y.405, W.406, Q.409, N.412, I.413, V.416, F.420 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.232, C:W.232, C:Y.405 Hydrogen bonds: C:R.292, C:R.292, C:Q.308 Salt bridges: C:R.292 PEF.14: 20 residues within 4Å: Chain C: E.503, R.506, V.507, L.508 Chain D: S.229, S.230, H.231, W.232, G.233, R.292, L.294, S.306, Q.308, H.402, Y.405, Q.409, N.412, I.413, V.416, F.420 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:E.503, C:E.503, D:R.292, D:R.292 Salt bridges: C:R.506 Hydrophobic interactions: D:W.232

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

NAG.2: 3 residues within 4Å: Chain A: N.180, K.194, E.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.180, A:E.195, A:E.195 NAG.3: 5 residues within 4Å: Chain A: P.212, N.214, S.260, K.263, N.264 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.214, A:N.214, A:S.260, A:K.263, A:K.263, A:N.264 NAG.4: 4 residues within 4Å: Chain A: R.172, D.225, L.226, N.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.172, A:D.225 NAG.7: 3 residues within 4Å: Chain B: N.180, K.194, E.195 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.180, B:E.195, B:E.195 NAG.8: 5 residues within 4Å: Chain B: P.212, N.214, S.260, K.263, N.264 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.214, B:N.214, B:S.260, B:K.263, B:K.263, B:N.264 NAG.9: 4 residues within 4Å: Chain B: R.172, D.225, L.226, N.227 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.172, B:D.225 NAG.11: 3 residues within 4Å: Chain C: N.180, K.194, E.195 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.180, C:E.195, C:E.195 NAG.12: 5 residues within 4Å: Chain C: P.212, N.214, S.260, K.263, N.264 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.214, C:N.214, C:S.260, C:K.263, C:K.263, C:N.264 NAG.13: 4 residues within 4Å: Chain C: R.172, D.225, L.226, N.227 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.172, C:D.225 NAG.15: 3 residues within 4Å: Chain D: N.180, K.194, E.195 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.180, D:E.195, D:E.195 NAG.16: 5 residues within 4Å: Chain D: P.212, N.214, S.260, K.263, N.264 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.214, D:N.214, D:S.260, D:K.263, D:K.263, D:N.264 NAG.17: 4 residues within 4Å: Chain D: R.172, D.225, L.226, N.227 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.172, D:D.225

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: L.493 Chain B: L.493 Chain C: L.493 Chain D: L.493 No protein-ligand interaction detected (PLIP)

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

2024-04-03

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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