SMTL ID : 7phk.1

Human voltage-gated potassium channel Kv3.1 in dimeric state (with Zn)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

16 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE(Non-covalent)

PCF.1: 9 residues within 4Å: Chain A: Q.409, W.411, M.414, L.415, A.418 Chain C: I.349, P.388, I.389, V.395 Ligand excluded by PLIP PCF.2: 4 residues within 4Å: Chain A: N.276, S.277, L.331, R.332 Ligand excluded by PLIP PCF.8: 9 residues within 4Å: Chain B: Q.409, W.411, M.414, L.415, A.418 Chain D: I.349, P.388, I.389, V.395 Ligand excluded by PLIP PCF.9: 4 residues within 4Å: Chain B: N.276, S.277, L.331, R.332 Ligand excluded by PLIP PCF.12: 10 residues within 4Å: Chain B: I.349, L.352, P.388, I.389, V.395 Chain C: Q.409, W.411, M.414, L.415, A.418 Ligand excluded by PLIP PCF.13: 4 residues within 4Å: Chain C: N.276, S.277, L.331, R.332 Ligand excluded by PLIP PCF.15: 10 residues within 4Å: Chain A: I.349, L.352, P.388, I.389, V.395 Chain D: Q.409, W.411, M.414, L.415, A.418 Ligand excluded by PLIP PCF.16: 4 residues within 4Å: Chain D: N.276, S.277, L.331, R.332 Ligand excluded by PLIP PCF.17: 10 residues within 4Å: Chain E: Q.409, W.411, M.414, L.415, A.418 Chain G: I.349, L.352, P.388, I.389, V.395 Ligand excluded by PLIP PCF.18: 4 residues within 4Å: Chain E: N.276, S.277, L.331, R.332 Ligand excluded by PLIP PCF.24: 9 residues within 4Å: Chain F: Q.409, W.411, M.414, L.415, A.418 Chain H: I.349, P.388, I.389, V.395 Ligand excluded by PLIP PCF.25: 4 residues within 4Å: Chain F: N.276, S.277, L.331, R.332 Ligand excluded by PLIP PCF.28: 10 residues within 4Å: Chain F: I.349, P.388, I.389, V.395 Chain G: Q.409, W.411, M.414, L.415, A.418 Chain H: H.212 Ligand excluded by PLIP PCF.29: 4 residues within 4Å: Chain G: N.276, S.277, L.331, R.332 Ligand excluded by PLIP PCF.31: 9 residues within 4Å: Chain E: I.349, P.388, I.389, V.395 Chain H: Q.409, W.411, M.414, L.415, A.418 Ligand excluded by PLIP PCF.32: 4 residues within 4Å: Chain H: N.276, S.277, L.331, R.332 Ligand excluded by PLIP

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.77, C.104, C.105 Chain C: C.83 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.77, A:C.104, A:C.105, C:C.83 ZN.10: 4 residues within 4Å: Chain B: H.77, C.104, C.105 Chain D: C.83 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Metal complexes: B:H.77, B:C.104, B:C.105, D:C.83 ZN.11: 4 residues within 4Å: Chain B: C.83 Chain C: H.77, C.104, C.105 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.77, C:C.104, C:C.105, B:C.83 ZN.14: 4 residues within 4Å: Chain A: C.83 Chain D: H.77, C.104, C.105 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:H.77, D:C.104, D:C.105, A:C.83 ZN.19: 4 residues within 4Å: Chain E: H.77, C.104, C.105 Chain G: C.83 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain G Metal complexes: E:H.77, E:C.104, E:C.105, G:C.83 ZN.26: 4 residues within 4Å: Chain F: H.77, C.104, C.105 Chain H: C.83 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain H Metal complexes: F:H.77, F:C.104, F:C.105, H:C.83 ZN.27: 4 residues within 4Å: Chain F: C.83 Chain G: H.77, C.104, C.105 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain F Metal complexes: G:H.77, G:C.104, G:C.105, F:C.83 ZN.30: 4 residues within 4Å: Chain E: C.83 Chain H: H.77, C.104, C.105 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain H Metal complexes: E:C.83, H:H.77, H:C.104, H:C.105

8 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: T.400 Chain B: T.400 Chain C: T.400 Chain D: T.400 Ligands: K.5 No protein-ligand interaction detected (PLIP) K.5: 10 residues within 4Å: Chain A: T.400, L.401 Chain B: T.400, L.401 Chain C: T.400, L.401 Chain D: T.400, L.401 Ligands: K.4, K.6 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Metal complexes: A:T.400, A:L.401, C:T.400, C:L.401, B:L.401 K.6: 10 residues within 4Å: Chain A: L.401, G.402 Chain B: L.401, G.402 Chain C: L.401, G.402 Chain D: L.401, G.402 Ligands: K.5, K.7 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: D:L.401, A:L.401, A:G.402, B:L.401, C:L.401 K.7: 9 residues within 4Å: Chain A: G.402, Y.403 Chain B: G.402, Y.403 Chain C: G.402, Y.403 Chain D: G.402, Y.403 Ligands: K.6 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:G.402, A:Y.403, D:G.402, C:Y.403, B:Y.403 K.20: 5 residues within 4Å: Chain E: T.400 Chain F: T.400 Chain G: T.400 Chain H: T.400 Ligands: K.21 No protein-ligand interaction detected (PLIP) K.21: 10 residues within 4Å: Chain E: T.400, L.401 Chain F: T.400, L.401 Chain G: T.400, L.401 Chain H: T.400, L.401 Ligands: K.20, K.22 5 PLIP interactions: 1 interactions with chain G, 2 interactions with chain E, 1 interactions with chain F, 1 interactions with chain H Metal complexes: G:T.400, E:T.400, E:L.401, F:T.400, H:T.400 K.22: 10 residues within 4Å: Chain E: L.401, G.402 Chain F: L.401, G.402 Chain G: L.401, G.402 Chain H: L.401, G.402 Ligands: K.21, K.23 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G, 1 interactions with chain F, 2 interactions with chain E Metal complexes: H:L.401, G:L.401, F:L.401, E:L.401, E:G.402 K.23: 9 residues within 4Å: Chain E: G.402, Y.403 Chain F: G.402, Y.403 Chain G: G.402, Y.403 Chain H: G.402, Y.403 Ligands: K.22 5 PLIP interactions: 1 interactions with chain F, 2 interactions with chain G, 1 interactions with chain E, 1 interactions with chain H Metal complexes: F:Y.403, G:G.402, G:Y.403, E:Y.403, H:Y.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chi, G. et al., Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain. Nat Commun (2022)

Release Date

2022-03-02

Peptides

Potassium voltage-gated channel, Shaw-related subfamily, member 1: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

E
E

F
G

G
F

H
H

Membrane

We predict this structure to be a membrane protein.
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Potassium voltage-gated channel, Shaw-related subfamily, member 1

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