SMTL ID : 8qz3.1

Crystal structure of human two pore domain potassium ion channel TREK-2 (K2P10.1) in complex with an activatory nanobody (Nb67)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-3-mer

Ligands

5 x K: POTASSIUM ION(Non-covalent)

K.1: 7 residues within 4Å: Chain A: V.71, Y.102, G.103, F.211, G.212 Chain B: F.211 Ligands: K.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.102 K.2: 11 residues within 4Å: Chain A: G.101, Y.102, G.103, G.210, F.211 Chain B: G.101, Y.102, G.210, F.211 Ligands: K.1, K.4 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:Y.102, B:F.211, A:Y.102, A:G.210, A:F.211 K.3: 5 residues within 4Å: Chain A: T.99, T.208 Chain B: T.99, T.208 Ligands: K.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:T.99, A:T.99, A:T.208, B:T.99, B:T.208 K.4: 10 residues within 4Å: Chain A: I.100, G.101, V.209, G.210 Chain B: I.100, G.101, V.209, G.210 Ligands: K.2, K.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:I.100, B:G.101, B:G.210, A:G.101, A:V.209 K.5: 10 residues within 4Å: Chain A: T.99, I.100, T.208, V.209 Chain B: T.99, I.100, T.208, V.209 Ligands: K.3, K.4 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:I.100, B:T.208, B:V.209, A:T.99, A:I.100

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 8 residues within 4Å: Chain A: F.129 Chain B: R.255, S.258, K.259, K.262 Chain D: Y.59, T.107, T.109 9 PLIP interactions: 3 interactions with chain B, 5 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: B:R.255, B:K.259, B:K.262, D:Y.59, D:T.109, A:F.129 Hydrogen bonds: D:Y.59, D:T.109 Water bridges: D:T.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodstrom, K.E.J. et al., Extracellular modulation of TREK-2 activity with nanobodies provides insight into the mechanisms of K2P channel regulation. Nat Commun (2024)

Release Date

2024-05-29

Peptides

Potassium channel subfamily K member 10: AB
Nanobody 67: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Potassium channel subfamily K member 10

Nanobody 67

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