SMTL ID : 8j01.1

Human KCNQ2-CaM in complex with CBD and PIP2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

8 x P0T: cannabidiol(Non-covalent)

P0T.1: 18 residues within 4Å: Chain A: L.237, I.238, S.241, F.242 Chain F: L.159, V.163, L.170, A.173, W.174, G.177, F.178, L.181, F.242, F.243, P.246, L.250 Ligands: P0T.2, PIO.9 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:L.170, F:W.174, F:F.178, F:F.243, F:F.243, F:P.246, F:L.250, A:L.237 P0T.2: 17 residues within 4Å: Chain A: W.226, R.229, L.230, A.233, T.234, L.237, I.238 Chain D: F.38, F.42 Chain F: W.174, F.178, L.181, L.206, W.207, L.210 Ligands: P0T.1, PIO.9 4 PLIP interactions: 1 interactions with chain F, 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: F:W.174 Hydrophobic interactions: A:A.233, A:I.238, D:F.42 P0T.5: 18 residues within 4Å: Chain A: L.159, V.163, L.170, A.173, W.174, G.177, F.178, L.181, F.242, F.243, P.246, L.250 Chain B: L.237, I.238, S.241, F.242 Ligands: P0T.6, PIO.12 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:L.237, A:L.170, A:W.174, A:F.178, A:F.243, A:F.243, A:P.246, A:L.250 Hydrogen bonds: A:L.170 P0T.6: 18 residues within 4Å: Chain A: W.174, F.178, L.181, A.203, L.206, W.207, L.210 Chain B: W.226, R.229, L.230, A.233, T.234, L.237, I.238 Chain F: F.38, F.42 Ligands: P0T.5, PIO.12 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: B:L.230, B:A.233, B:I.238, F:F.42 Hydrogen bonds: A:W.174 P0T.7: 18 residues within 4Å: Chain B: L.159, V.163, L.170, A.173, W.174, G.177, F.178, L.181, F.242, F.243, P.246, L.250 Chain D: L.237, I.238, S.241, F.242 Ligands: PIO.3, P0T.8 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.170, B:W.174, B:F.178, B:F.243, B:F.243, B:F.243, B:P.246, B:L.250 Hydrogen bonds: B:L.170 P0T.8: 18 residues within 4Å: Chain A: F.38, F.42 Chain B: W.174, F.178, L.181, A.203, L.206, W.207, L.210 Chain D: W.226, R.229, L.230, A.233, T.234, L.237, I.238 Ligands: PIO.3, P0T.7 8 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: D:L.230, D:A.233, D:I.238, A:F.42, B:W.174, B:L.210 Hydrogen bonds: D:T.234, B:W.174 P0T.10: 18 residues within 4Å: Chain D: L.159, V.163, L.170, A.173, W.174, G.177, F.178, L.181, F.242, F.243, P.246, L.250 Chain F: L.237, I.238, S.241, F.242 Ligands: PIO.4, P0T.11 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.170, D:W.174, D:F.178, D:F.243, D:F.243, D:P.246, D:L.250 Hydrogen bonds: D:L.170 P0T.11: 18 residues within 4Å: Chain B: F.38, F.42 Chain D: W.174, F.178, L.181, A.203, L.206, W.207, L.210 Chain F: W.226, R.229, L.230, A.233, T.234, L.237, I.238 Ligands: PIO.4, P0T.10 7 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: F:L.230, F:A.233, F:I.238, B:F.42, D:W.174 Hydrogen bonds: F:T.234, D:W.174

4 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Covalent)

PIO.3: 19 residues within 4Å: Chain A: R.25, R.27, F.31, A.35, F.38, M.146, M.149, D.150, R.152, G.154, T.155, K.265 Chain B: S.167, K.168, V.171, W.174, Y.175 Ligands: P0T.7, P0T.8 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.31, A:F.38, A:T.155, B:V.171, B:Y.175 Hydrogen bonds: A:R.152, A:R.152 Salt bridges: A:R.25, A:R.25, A:R.152, A:K.265, A:K.265, B:K.168 PIO.4: 21 residues within 4Å: Chain B: R.25, R.27, F.31, A.35, F.38, M.146, M.149, D.150, R.152, G.154, T.155, H.262, K.265 Chain D: S.167, K.168, V.171, T.172, W.174, Y.175 Ligands: P0T.10, P0T.11 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain B Hydrophobic interactions: D:V.171, D:Y.175, B:F.38, B:T.155 Salt bridges: D:K.168, B:R.25, B:R.25, B:R.152, B:K.265, B:K.265 Hydrogen bonds: B:R.152, B:R.152 PIO.9: 20 residues within 4Å: Chain D: R.25, R.27, F.31, A.35, F.38, M.149, D.150, R.152, G.154, T.155, H.262, K.265 Chain F: S.167, K.168, V.171, T.172, W.174, Y.175 Ligands: P0T.1, P0T.2 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:F.31, D:F.38, D:T.155, F:V.171, F:Y.175 Hydrogen bonds: D:R.152, D:R.152 Salt bridges: D:R.25, D:R.25, D:R.152, D:K.265, D:K.265, F:K.168 PIO.12: 20 residues within 4Å: Chain A: S.167, K.168, V.171, W.174, Y.175 Chain F: R.25, R.27, F.31, A.35, F.38, M.146, M.149, D.150, R.152, G.154, T.155, H.262, K.265 Ligands: P0T.5, P0T.6 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:F.31, F:F.38, F:T.155, A:V.171, A:Y.175 Hydrogen bonds: F:R.152, F:R.152 Salt bridges: F:R.25, F:R.25, F:R.152, F:K.265, F:K.265, A:K.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, D. et al., Ligand activation mechanisms of human KCNQ2 channel. Nat Commun (2023)

Release Date

2023-12-13

Peptides

Potassium voltage-gated channel subfamily KQT member 2: ABDF
Calmodulin-1: CEGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

F
G

C
C

E
F

G
H

H
E

Membrane

We predict this structure to be a membrane protein.
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Potassium voltage-gated channel subfamily KQT member 2

Calmodulin-1

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