SMTL ID : 9jgz.1

Cryo-EM Structure of Human Kcnk13.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

12 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)(Non-functional Binders)

POV.1: 4 residues within 4Å: Chain A: F.93, R.250 Ligands: POV.2, EIC.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.93 Hydrogen bonds: A:R.250 POV.2: 1 residues within 4Å: Ligands: POV.1 No protein-ligand interaction detected (PLIP) POV.6: 5 residues within 4Å: Chain A: F.137, R.140, I.144, M.259 Chain B: N.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.137, A:I.144 Hydrogen bonds: B:N.9 POV.7: 2 residues within 4Å: Chain A: L.141, I.148 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.141 POV.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) POV.9: 3 residues within 4Å: Chain A: L.5, N.9, L.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.9 POV.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) POV.13: 3 residues within 4Å: Chain B: L.5, N.9, L.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.13 Hydrogen bonds: B:N.9 POV.14: 4 residues within 4Å: Chain B: F.93, R.250 Ligands: POV.15, EIC.16 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.93 Hydrogen bonds: B:R.250 POV.15: 1 residues within 4Å: Ligands: POV.14 No protein-ligand interaction detected (PLIP) POV.19: 4 residues within 4Å: Chain B: F.137, R.140, I.144, M.259 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.137, B:I.144 Hydrogen bonds: A:N.9 POV.20: 2 residues within 4Å: Chain B: L.141, I.148 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.141

2 x EIC: LINOLEIC ACID(Non-covalent)

EIC.3: 15 residues within 4Å: Chain A: F.93, Y.94, G.97, S.101, T.130, F.133, S.238, R.250, N.253, F.254, I.257, L.258 Chain B: I.19, V.20 Ligands: POV.1 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.93, A:Y.94, A:Y.94, A:T.130, A:F.133, A:F.254, A:F.254, A:I.257, A:L.258, B:I.19, B:V.20 Hydrogen bonds: A:S.238, A:N.253 Salt bridges: A:R.84 EIC.16: 15 residues within 4Å: Chain A: I.19, V.20 Chain B: F.93, Y.94, G.97, S.101, T.130, F.133, S.238, R.250, N.253, F.254, I.257, L.258 Ligands: POV.14 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.93, B:Y.94, B:Y.94, B:T.130, B:F.133, B:F.254, B:F.254, B:I.257, B:L.258, A:I.19, A:V.20 Hydrogen bonds: B:S.238, B:N.253 Salt bridges: B:R.84

2 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.4: 4 residues within 4Å: Chain A: S.201, F.217, F.224 Chain B: I.117 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.117, A:F.217, A:F.224 ACD.17: 4 residues within 4Å: Chain A: I.117 Chain B: S.201, F.217, F.224 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.217, B:F.224, A:I.117

2 x D21: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate(Non-covalent)

D21.5: 6 residues within 4Å: Chain A: Y.22, Y.187, I.275, S.278, W.281 Chain B: S.129 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.22, A:I.275, A:W.281 D21.18: 6 residues within 4Å: Chain A: S.129 Chain B: Y.22, Y.187, I.275, S.278, W.281 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.22, B:I.275, B:W.281

4 x K: POTASSIUM ION(Non-covalent)

K.10: 10 residues within 4Å: Chain A: I.103, G.104, I.230, G.231 Chain B: I.103, G.104, I.230, G.231 Ligands: K.21, K.22 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:I.103, B:G.104, B:I.230, A:I.103, A:G.104 K.11: 5 residues within 4Å: Chain A: T.102, T.229 Chain B: T.102, T.229 Ligands: K.22 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:T.102, A:T.229, B:T.102, B:T.229 K.21: 9 residues within 4Å: Chain A: G.104, F.105, G.231, F.232 Chain B: G.104, F.105, G.231, F.232 Ligands: K.10 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:G.104, B:F.105, B:G.231, A:G.104, A:G.231 K.22: 10 residues within 4Å: Chain A: T.102, I.103, T.229, I.230 Chain B: T.102, I.103, T.229, I.230 Ligands: K.10, K.11 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:T.102, B:I.103, A:T.102, A:I.103, A:I.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fang, X. et al., Gating mechanism of the two-pore-domain potassium channel THIK1. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-05-07

Peptides

Potassium channel subfamily K member 13: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Potassium channel subfamily K member 13