SMTL ID : 9bws.1

Structure of human k2P13.1 (THIK-1) S136P Y273A in lipid nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x D12: DODECANE(Non-covalent)

D12.1: 9 residues within 4Å: Chain A: F.101, G.255, R.258, F.259, F.262 Chain B: V.28, L.32 Ligands: OCT.3, EIC.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.101, A:F.101 D12.12: 9 residues within 4Å: Chain A: V.28 Chain B: F.101, G.255, R.258, F.259, F.262 Ligands: OCT.8, OCT.15, EIC.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.101

4 x D10: DECANE(Non-functional Binders)(Non-covalent)

D10.2: 3 residues within 4Å: Chain A: L.256, A.260 Ligands: D10.5 No protein-ligand interaction detected (PLIP) D10.5: 4 residues within 4Å: Chain A: C.211, A.214, M.215 Ligands: D10.2 No protein-ligand interaction detected (PLIP) D10.13: 7 residues within 4Å: Chain B: M.215, I.219, L.256, Y.257, A.260, F.264 Ligands: D10.16 No protein-ligand interaction detected (PLIP) D10.16: 7 residues within 4Å: Chain B: C.211, A.214, M.215, P.218, I.219, F.264 Ligands: D10.13 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.218

8 x OCT: N-OCTANE(Non-functional Binders)

OCT.3: 2 residues within 4Å: Chain A: F.97 Ligands: D12.1 No protein-ligand interaction detected (PLIP) OCT.4: 3 residues within 4Å: Chain A: G.255, L.256, F.259 No protein-ligand interaction detected (PLIP) OCT.8: 3 residues within 4Å: Chain A: L.32 Chain B: F.97 Ligands: D12.12 No protein-ligand interaction detected (PLIP) OCT.9: 2 residues within 4Å: Chain A: L.21 Ligands: OCT.14 No protein-ligand interaction detected (PLIP) OCT.11: 4 residues within 4Å: Chain A: F.145, I.152 Chain B: N.17 Ligands: OCT.17 No protein-ligand interaction detected (PLIP) OCT.14: 5 residues within 4Å: Chain A: N.17 Chain B: F.145, R.148, I.152 Ligands: OCT.9 No protein-ligand interaction detected (PLIP) OCT.15: 4 residues within 4Å: Chain B: G.255, L.256, F.259 Ligands: D12.12 No protein-ligand interaction detected (PLIP) OCT.17: 3 residues within 4Å: Chain B: L.21 Ligands: EIC.7, OCT.11 No protein-ligand interaction detected (PLIP)

2 x HEX: HEXANE(Non-covalent)(Non-functional Binders)

HEX.6: 4 residues within 4Å: Chain A: L.32, G.33, A.36 Chain B: F.97 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.97 HEX.18: 4 residues within 4Å: Chain A: F.97 Chain B: L.32, G.33, A.36 No protein-ligand interaction detected (PLIP)

2 x EIC: LINOLEIC ACID(Non-covalent)

EIC.7: 21 residues within 4Å: Chain A: R.92, Y.102, G.105, T.106, V.108, S.109, I.111, T.138, F.141, S.246, R.258, N.261, F.262, I.265, L.266 Chain B: A.24, I.27, V.28, L.31 Ligands: D12.1, OCT.17 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.102, A:Y.102, A:T.138, A:F.141, A:F.141, A:F.262, A:I.265, A:L.266, B:I.27 Hydrogen bonds: A:S.246, A:N.261 Salt bridges: A:R.92 EIC.19: 20 residues within 4Å: Chain A: A.24, I.27, V.28, L.31 Chain B: R.92, Y.102, G.105, T.106, V.108, S.109, I.111, T.138, F.141, S.246, R.258, N.261, F.262, I.265, L.266 Ligands: D12.12 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.102, B:Y.102, B:T.138, B:F.141, B:F.262, B:I.265, B:L.266, A:I.27 Hydrogen bonds: B:S.246, B:N.261 Salt bridges: B:R.92

4 x K: POTASSIUM ION(Non-covalent)

K.10: 5 residues within 4Å: Chain A: T.110, T.237 Chain B: T.110, T.237 Ligands: K.21 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:T.110, A:T.237, B:T.110, B:T.237 K.20: 9 residues within 4Å: Chain A: G.112, F.113, G.239, F.240 Chain B: G.112, F.113, G.239, F.240 Ligands: K.22 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:G.112, A:G.239, B:G.239 K.21: 10 residues within 4Å: Chain A: T.110, I.111, T.237, I.238 Chain B: T.110, I.111, T.237, I.238 Ligands: K.10, K.22 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:I.111, B:I.238, A:I.111, A:I.238 K.22: 10 residues within 4Å: Chain A: I.111, G.112, I.238, G.239 Chain B: I.111, G.112, I.238, G.239 Ligands: K.20, K.21 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:I.111, B:I.238, A:I.111, A:G.112, A:G.239

Links

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Citation

Roy-Chowdhury, S. et al., Structure of the human K 2P 13.1 channel reveals a hydrophilic pore restriction and lipid cofactor site. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-02-26

Peptides

Potassium channel subfamily K member 13: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
U

B
A

Membrane

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