SMTL ID : 5mkf.1

cryoEM Structure of Polycystin-2 in complex with calcium and lipids

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: D.373, L.374, N.375 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: D.373, L.374, N.375 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: D.373, L.374, N.375 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain D: D.373, L.374, N.375 No protein-ligand interaction detected (PLIP)

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

NAG.5: 5 residues within 4Å: Chain A: N.328, G.329, K.342, E.343, C.344 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.328, A:G.329, A:C.344, A:C.344 NAG.6: 3 residues within 4Å: Chain A: P.360, R.361, N.362 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.360, A:N.362 NAG.7: 3 residues within 4Å: Chain A: S.298, N.299, T.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.299, A:T.301 NAG.18: 5 residues within 4Å: Chain B: N.328, G.329, K.342, E.343, C.344 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.328, B:G.329, B:C.344, B:C.344 NAG.19: 3 residues within 4Å: Chain B: P.360, R.361, N.362 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.360, B:N.362 NAG.20: 3 residues within 4Å: Chain B: S.298, N.299, T.301 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.299, B:T.301 NAG.28: 5 residues within 4Å: Chain C: N.328, G.329, K.342, E.343, C.344 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.328, C:G.329, C:C.344, C:C.344 NAG.29: 3 residues within 4Å: Chain C: P.360, R.361, N.362 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.360, C:N.362 NAG.30: 3 residues within 4Å: Chain C: S.298, N.299, T.301 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.299, C:T.301 NAG.37: 5 residues within 4Å: Chain D: N.328, G.329, K.342, E.343, C.344 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.328, D:G.329, D:C.344, D:C.344 NAG.38: 3 residues within 4Å: Chain D: P.360, R.361, N.362 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:P.360, D:N.362 NAG.39: 3 residues within 4Å: Chain D: S.298, N.299, T.301 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.299, D:T.301

4 x PX6: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX6.8: 5 residues within 4Å: Chain A: W.380, Q.557, N.560 Chain B: N.653, V.655 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.655 PX6.21: 5 residues within 4Å: Chain B: W.380, Q.557, N.560 Chain C: N.653, V.655 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.655 PX6.31: 5 residues within 4Å: Chain C: W.380, Q.557, N.560 Chain D: N.653, V.655 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.655 PX6.40: 5 residues within 4Å: Chain A: N.653, V.655 Chain D: W.380, Q.557, N.560 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.655

12 x PLM: PALMITIC ACID(Non-covalent)

PLM.9: 5 residues within 4Å: Chain A: W.507, F.567, F.574 Chain B: Y.611, F.667 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.667, A:F.567 PLM.10: 4 residues within 4Å: Chain A: W.380, Q.630 Chain B: F.666 Ligands: PLM.11 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.666 Hydrogen bonds: A:Q.630, A:Q.630 PLM.11: 4 residues within 4Å: Chain A: F.605, Q.630 Ligands: PLM.10, CHS.44 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.605, A:F.605 Hydrogen bonds: A:Q.630 PLM.22: 5 residues within 4Å: Chain B: W.507, F.567, F.574 Chain C: Y.611, F.667 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.667, B:F.567 PLM.23: 3 residues within 4Å: Chain B: W.380, Q.630 Ligands: PLM.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.630, B:Q.630 PLM.24: 4 residues within 4Å: Chain B: F.605, Q.630 Ligands: CHS.12, PLM.23 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.605, B:F.605 Hydrogen bonds: B:Q.630 PLM.32: 5 residues within 4Å: Chain C: W.507, F.567, F.574 Chain D: Y.611, F.667 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.667, C:F.567 PLM.33: 3 residues within 4Å: Chain C: W.380, Q.630 Ligands: PLM.34 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.630, C:Q.630 PLM.34: 4 residues within 4Å: Chain C: F.605, Q.630 Ligands: CHS.25, PLM.33 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.605, C:F.605 Hydrogen bonds: C:Q.630 PLM.41: 5 residues within 4Å: Chain A: Y.611, F.667 Chain D: W.507, F.567, F.574 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.567, A:F.667 PLM.42: 3 residues within 4Å: Chain A: F.666 Chain D: W.380, Q.630 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.666 Hydrogen bonds: D:Q.630, D:Q.630 PLM.43: 3 residues within 4Å: Chain D: F.605, Q.630 Ligands: CHS.35 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.605, D:F.605 Hydrogen bonds: D:Q.630

8 x CHS: 4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID(Non-covalent)

CHS.12: 5 residues within 4Å: Chain A: T.238, Y.239 Chain B: Q.613, F.629 Ligands: PLM.24 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.613, B:Q.613, A:T.238 CHS.13: 5 residues within 4Å: Chain A: L.231, I.232, C.235, I.236, Y.239 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.231, A:I.232 Hydrogen bonds: A:C.235 CHS.25: 5 residues within 4Å: Chain B: T.238, Y.239 Chain C: Q.613, F.629 Ligands: PLM.34 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.238, B:Y.239, C:Q.613 CHS.26: 5 residues within 4Å: Chain B: L.231, I.232, C.235, I.236, Y.239 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.231, B:I.232 Hydrogen bonds: B:C.235 CHS.35: 5 residues within 4Å: Chain C: T.238, Y.239 Chain D: Q.613, F.629 Ligands: PLM.43 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.238, D:Q.613 CHS.36: 5 residues within 4Å: Chain C: L.231, I.232, C.235, I.236, Y.239 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.231, C:I.232 Hydrogen bonds: C:C.235 CHS.44: 5 residues within 4Å: Chain A: Q.613, F.629 Chain D: T.238, Y.239 Ligands: PLM.11 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:T.238, A:Q.613 CHS.45: 5 residues within 4Å: Chain D: L.231, I.232, C.235, I.236, Y.239 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.231, D:I.232 Hydrogen bonds: D:C.235

5 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.14: 4 residues within 4Å: Chain A: N.681 Chain B: N.681 Chain C: N.681 Chain D: N.681 No protein-ligand interaction detected (PLIP) CA.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.27: 4 residues within 4Å: Chain A: L.641 Chain B: L.641 Chain C: L.641 Chain D: L.641 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilkes, M. et al., Molecular insights into lipid-assisted Ca(2+) regulation of the TRP channel Polycystin-2. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-01-18

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.
Show / Hide

Polycystin-2

Related Entries With Identical Sequence