SMTL ID : 7bym.1

Cryo-EM structure of human KCNQ4 with retigabine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x PT5: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)

PT5.1: 13 residues within 4Å: Chain A: L.375, E.376, P.378, F.383, H.386, V.387, F.390, R.434, K.456, F.458, R.500, M.501, R.503 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.387, A:F.390, A:R.503 Hydrogen bonds: A:E.376, A:R.434, A:R.434, A:R.500, A:R.503 Water bridges: A:E.430, A:E.430 Salt bridges: A:H.386, A:H.386, A:R.434, A:K.456, A:R.503, A:R.503 PT5.7: 12 residues within 4Å: Chain B: L.375, E.376, P.378, H.386, V.387, F.390, R.434, K.456, F.458, R.500, M.501, R.503 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.387, B:F.390, B:R.503 Hydrogen bonds: B:E.376, B:R.434, B:R.434, B:R.500, B:R.503 Water bridges: B:E.430, B:R.500 Salt bridges: B:H.386, B:H.386, B:R.434, B:K.456, B:R.503, B:R.503 PT5.9: 13 residues within 4Å: Chain C: L.375, E.376, P.378, F.383, H.386, V.387, F.390, R.434, K.456, F.458, R.500, M.501, R.503 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:V.387, C:F.390, C:R.503 Hydrogen bonds: C:E.376, C:R.434, C:R.434, C:R.503 Water bridges: C:R.500 Salt bridges: C:H.386, C:H.386, C:R.434, C:K.456, C:K.456, C:R.503, C:R.503 PT5.11: 13 residues within 4Å: Chain D: L.375, E.376, P.378, F.383, H.386, V.387, F.390, R.434, K.456, F.458, R.500, M.501, R.503 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:V.387, D:F.390, D:R.503 Hydrogen bonds: D:E.376, D:R.434, D:R.434, D:R.500, D:R.503 Water bridges: D:E.430, D:E.430 Salt bridges: D:H.386, D:H.386, D:R.434, D:K.456, D:K.456, D:R.503, D:R.503

4 x FBX: ethyl N-[2-azanyl-4-[(4-fluorophenyl)methylamino]phenyl]carbamate(Non-covalent)

FBX.2: 8 residues within 4Å: Chain A: L.589, S.593 Chain C: F.394 Chain D: W.526, F.530, L.533, F.595, L.602 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:L.533, D:L.602, A:L.589 Hydrogen bonds: A:L.589, A:S.593, A:S.593 FBX.6: 9 residues within 4Å: Chain A: W.526, F.530, F.595, P.598, L.602 Chain B: L.589, L.590, S.593 Chain D: F.394 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.589, A:L.602 Hydrogen bonds: B:L.589, B:S.593, B:S.593 FBX.8: 9 residues within 4Å: Chain A: F.394 Chain B: W.526, F.530, L.533, F.595, L.602 Chain C: L.589, L.590, S.593 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:L.533, B:L.602, C:L.589 Hydrogen bonds: C:L.589, C:S.593, C:S.593 FBX.10: 10 residues within 4Å: Chain B: F.394 Chain C: W.526, F.530, L.533, F.595, P.598, L.602 Chain D: L.589, L.590, S.593 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.530, C:L.533, C:L.602, D:L.589 Hydrogen bonds: D:L.589, D:S.593, D:S.593

3 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: G.569, Y.570 Chain B: G.569, Y.570 Chain C: G.569, Y.570 Chain D: G.569, Y.570 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:G.569, C:Y.570, B:G.569 K.4: 8 residues within 4Å: Chain A: T.567, I.568 Chain B: T.567, I.568 Chain C: T.567, I.568 Chain D: T.567, I.568 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:I.568, D:I.568, B:I.568, A:I.568 K.5: 4 residues within 4Å: Chain A: T.567 Chain B: T.567 Chain C: T.567 Chain D: T.567 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.567

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, T. et al., Structural Basis for the Modulation of Human KCNQ4 by Small-Molecule Drugs. Mol.Cell (2021)

Release Date

2020-12-02

Peptides

Green fluorescent protein,Potassium voltage-gated channel subfamily KQT member 4: ABCD
Calmodulin-3: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

E
B

F
D

G
F

H
H

Membrane

We predict this structure to be a membrane protein.
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Green fluorescent protein,Potassium voltage-gated channel subfamily KQT member 4

Calmodulin-3

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