SMTL ID : 6t9o.1

CryoEM structure of human polycystin-2/PKD2 in UDM supplemented with PI(3,5)P2

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: 4 residues within 4Å: Chain A: R.137, L.191, N.192, Q.354 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: R.137, L.191, N.192, Q.354 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: R.137, L.191, N.192, Q.354 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: R.137, L.191, N.192, Q.354 No protein-ligand interaction detected (PLIP)

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

NAG.5: 3 residues within 4Å: Chain A: N.145, K.159, E.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.145 NAG.6: 3 residues within 4Å: Chain A: P.177, N.179, N.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.229 NAG.14: 3 residues within 4Å: Chain B: N.145, K.159, E.160 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.145 NAG.15: 3 residues within 4Å: Chain B: P.177, N.179, N.229 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.229 NAG.22: 3 residues within 4Å: Chain C: N.145, K.159, E.160 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.145 NAG.23: 3 residues within 4Å: Chain C: P.177, N.179, N.229 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.229 NAG.30: 3 residues within 4Å: Chain D: N.145, K.159, E.160 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.145 NAG.31: 3 residues within 4Å: Chain D: P.177, N.179, N.229 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.229

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 10 residues within 4Å: Chain A: Q.374, N.377, I.378, V.381 Chain B: V.472, L.473, I.476 Ligands: UMQ.8, UMQ.10, UMQ.11 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.473, B:I.476, A:I.378, A:V.381, A:V.381 Hydrogen bonds: A:Q.374, A:Q.374, A:N.377 CLR.16: 10 residues within 4Å: Chain B: Q.374, N.377, I.378, V.381 Chain C: V.472, L.473, I.476 Ligands: UMQ.17, UMQ.19, UMQ.20 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.378, B:V.381, B:V.381, C:L.473, C:I.476 Hydrogen bonds: B:Q.374, B:Q.374, B:N.377 CLR.24: 10 residues within 4Å: Chain C: Q.374, N.377, I.378, V.381 Chain D: V.472, L.473, I.476 Ligands: UMQ.25, UMQ.27, UMQ.28 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.378, C:V.381, C:V.381, D:V.472, D:L.473, D:I.476 Hydrogen bonds: C:Q.374, C:Q.374, C:N.377 CLR.32: 10 residues within 4Å: Chain A: V.472, L.473, I.476 Chain D: Q.374, N.377, I.378, V.381 Ligands: UMQ.33, UMQ.35, UMQ.36 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:V.472, A:L.473, A:I.476, D:I.378, D:V.381, D:V.381 Hydrogen bonds: D:Q.374, D:Q.374, D:N.377

20 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.8: 13 residues within 4Å: Chain A: H.196, W.197, Q.273, Y.370, I.373, Q.374, N.377 Chain B: N.470, R.471, V.472 Ligands: CLR.7, UMQ.10, UMQ.11 Ligand excluded by PLIP UMQ.9: 13 residues within 4Å: Chain A: L.51, T.55, M.58, Y.282, E.294, I.295, F.297, I.339, N.342, I.343, S.347, F.375, A.379 Ligand excluded by PLIP UMQ.10: 6 residues within 4Å: Chain A: W.197, T.202 Chain B: I.476 Ligands: CLR.7, UMQ.8, UMQ.12 Ligand excluded by PLIP UMQ.11: 6 residues within 4Å: Chain A: L.334, Y.370, W.371, Q.374 Ligands: CLR.7, UMQ.8 Ligand excluded by PLIP UMQ.12: 6 residues within 4Å: Chain A: W.197, Q.447, F.451 Chain B: R.471, I.476 Ligands: UMQ.10 Ligand excluded by PLIP UMQ.17: 13 residues within 4Å: Chain B: H.196, W.197, Q.273, Y.370, I.373, Q.374, N.377 Chain C: N.470, R.471, V.472 Ligands: CLR.16, UMQ.19, UMQ.20 Ligand excluded by PLIP UMQ.18: 13 residues within 4Å: Chain B: L.51, T.55, M.58, Y.282, E.294, I.295, F.297, I.339, N.342, I.343, S.347, F.375, A.379 Ligand excluded by PLIP UMQ.19: 6 residues within 4Å: Chain B: W.197, T.202 Chain C: I.476 Ligands: CLR.16, UMQ.17, UMQ.21 Ligand excluded by PLIP UMQ.20: 6 residues within 4Å: Chain B: L.334, Y.370, W.371, Q.374 Ligands: CLR.16, UMQ.17 Ligand excluded by PLIP UMQ.21: 6 residues within 4Å: Chain B: W.197, Q.447, F.451 Chain C: R.471, I.476 Ligands: UMQ.19 Ligand excluded by PLIP UMQ.25: 13 residues within 4Å: Chain C: H.196, W.197, Q.273, Y.370, I.373, Q.374, N.377 Chain D: N.470, R.471, V.472 Ligands: CLR.24, UMQ.27, UMQ.28 Ligand excluded by PLIP UMQ.26: 13 residues within 4Å: Chain C: L.51, T.55, M.58, Y.282, E.294, I.295, F.297, I.339, N.342, I.343, S.347, F.375, A.379 Ligand excluded by PLIP UMQ.27: 6 residues within 4Å: Chain C: W.197, T.202 Chain D: I.476 Ligands: CLR.24, UMQ.25, UMQ.29 Ligand excluded by PLIP UMQ.28: 6 residues within 4Å: Chain C: L.334, Y.370, W.371, Q.374 Ligands: CLR.24, UMQ.25 Ligand excluded by PLIP UMQ.29: 6 residues within 4Å: Chain C: W.197, Q.447, F.451 Chain D: R.471, I.476 Ligands: UMQ.27 Ligand excluded by PLIP UMQ.33: 14 residues within 4Å: Chain A: A.469, N.470, R.471, V.472 Chain D: H.196, W.197, Q.273, Y.370, I.373, Q.374, N.377 Ligands: CLR.32, UMQ.35, UMQ.36 Ligand excluded by PLIP UMQ.34: 13 residues within 4Å: Chain D: L.51, T.55, M.58, Y.282, E.294, I.295, F.297, I.339, N.342, I.343, S.347, F.375, A.379 Ligand excluded by PLIP UMQ.35: 6 residues within 4Å: Chain A: I.476 Chain D: W.197, T.202 Ligands: CLR.32, UMQ.33, UMQ.37 Ligand excluded by PLIP UMQ.36: 6 residues within 4Å: Chain D: L.334, Y.370, W.371, Q.374 Ligands: CLR.32, UMQ.33 Ligand excluded by PLIP UMQ.37: 6 residues within 4Å: Chain A: R.471, I.476 Chain D: W.197, Q.447, F.451 Ligands: UMQ.35 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 4 residues within 4Å: Chain A: L.458 Chain B: L.458 Chain C: L.458 Chain D: L.458 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., Lipid Interactions of a Ciliary Membrane TRP Channel: Simulation and Structural Studies of Polycystin-2. Structure (2020)

Release Date

2019-11-20

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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