SMTL ID : 9ed1.1

Cryo-EM structure of the human KCa3.1/calmodulin channel in complex with Ca2+ and 1,4-dihydropyridine (DHP-103)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

5 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.1: 9 residues within 4Å: Chain A: G.244, Y.245 Chain B: G.244, Y.245 Chain C: G.244, Y.245 Chain D: G.244, Y.245 Ligands: K.4 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: D:Y.245, A:Y.245, B:Y.245, C:G.244 K.2: 5 residues within 4Å: Chain A: T.242 Chain B: T.242 Chain C: T.242 Chain D: T.242 Ligands: K.5 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Metal complexes: C:T.242, B:T.242, D:T.242 K.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.4: 8 residues within 4Å: Chain A: G.244 Chain B: I.243, G.244 Chain C: I.243, G.244 Chain D: I.243, G.244 Ligands: K.1 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Metal complexes: A:G.244, C:I.243, C:G.244, B:G.244, D:G.244 K.5: 8 residues within 4Å: Chain A: T.242 Chain B: T.242, I.243 Chain C: T.242, I.243 Chain D: T.242, I.243 Ligands: K.2 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Metal complexes: C:T.242, A:T.242, B:T.242, D:T.242

12 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain E: D.18, D.20, D.22, T.24, E.29 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.18, E:D.22, E:D.22, E:T.24, E:E.29 CA.7: 5 residues within 4Å: Chain E: D.54, D.56, N.58, T.60, E.65 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.54, E:T.60, E:E.65 CA.8: 6 residues within 4Å: Chain E: D.91, D.93, N.95, Y.97, S.99, E.102 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.93, E:D.93 CA.9: 3 residues within 4Å: Chain F: D.22, T.24, E.29 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.22, F:D.22, F:T.24, F:E.29, F:E.29 CA.10: 3 residues within 4Å: Chain F: D.54, T.60, E.65 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.54, F:T.60, F:E.65 CA.11: 6 residues within 4Å: Chain F: D.91, D.93, N.95, Y.97, S.99, E.102 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.91, F:D.93, F:D.93, F:Y.97 CA.12: 5 residues within 4Å: Chain G: D.18, D.20, D.22, T.24, E.29 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.22, G:D.22, G:T.24, G:E.29, G:E.29 CA.13: 5 residues within 4Å: Chain G: D.54, D.56, N.58, T.60, E.65 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.54, G:T.60, G:E.65 CA.14: 6 residues within 4Å: Chain G: D.91, D.93, N.95, Y.97, S.99, E.102 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.93, G:D.93, G:E.102, G:E.102 CA.15: 4 residues within 4Å: Chain H: D.18, D.22, T.24, E.29 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.18, H:D.22, H:D.22, H:T.24, H:E.29 CA.16: 3 residues within 4Å: Chain H: D.54, T.60, E.65 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:D.54, H:T.60, H:E.65 CA.17: 6 residues within 4Å: Chain H: D.91, D.93, N.95, Y.97, S.99, E.102 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.93, H:D.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ong, S.T. et al., Design and structural basis of selective 1,4-dihydropyridine inhibitors of the calcium-activated potassium channel, KCa3.1. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-04-16

Peptides

Intermediate conductance calcium-activated potassium channel protein 4: ABCD
Calmodulin-1: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Intermediate conductance calcium-activated potassium channel protein 4

Calmodulin-1

Related Entries With Identical Sequence