SMTL ID : 4jtd.2 (1 other biounit)

Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Lys27Met mutant of Charybdotoxin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

hetero-4-4-1-mer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 33 residues within 4Å: Chain A: G.21, T.22, W.23, T.25, Q.29, D.51, Y.56, K.84, N.124, S.154, R.155, Q.180, W.209, S.210, P.211, L.212, A.213, C.214, G.215, S.218, K.220, Y.228, S.229, R.230, P.270, L.287, L.288, G.289, A.290, S.291, Q.295, E.298, N.299 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:W.23, A:W.209 Hydrogen bonds: A:T.22, A:W.23, A:Q.29, A:D.51, A:Y.56, A:K.84, A:S.154, A:S.154, A:R.155, A:S.210, A:L.212, A:C.214, A:S.218, A:K.220, A:R.230, A:R.230, A:R.230, A:L.288, A:S.291, A:S.291, A:Q.295, A:E.298, A:N.299 Water bridges: A:K.220, A:Y.228, A:G.289, A:G.289 Salt bridges: A:K.220, A:R.230, A:R.230 pi-Stacking: A:W.209 NAP.7: 33 residues within 4Å: Chain C: G.21, T.22, W.23, T.25, Q.29, D.51, Y.56, K.84, N.124, S.154, R.155, Q.180, W.209, S.210, P.211, L.212, A.213, C.214, G.215, S.218, K.220, Y.228, S.229, R.230, P.270, L.287, L.288, G.289, A.290, S.291, Q.295, E.298, N.299 33 PLIP interactions: 33 interactions with chain C Hydrophobic interactions: C:W.23, C:W.209 Hydrogen bonds: C:T.22, C:W.23, C:Q.29, C:D.51, C:Y.56, C:K.84, C:S.154, C:S.154, C:R.155, C:S.210, C:L.212, C:C.214, C:S.218, C:K.220, C:R.230, C:R.230, C:R.230, C:L.288, C:S.291, C:S.291, C:Q.295, C:E.298, C:N.299 Water bridges: C:K.220, C:Y.228, C:G.289, C:G.289 Salt bridges: C:K.220, C:R.230, C:R.230 pi-Stacking: C:W.209 NAP.13: 33 residues within 4Å: Chain E: G.21, T.22, W.23, T.25, Q.29, D.51, Y.56, K.84, N.124, S.154, R.155, Q.180, W.209, S.210, P.211, L.212, A.213, C.214, G.215, S.218, K.220, Y.228, S.229, R.230, P.270, L.287, L.288, G.289, A.290, S.291, Q.295, E.298, N.299 33 PLIP interactions: 33 interactions with chain E Hydrophobic interactions: E:W.23, E:W.209 Hydrogen bonds: E:T.22, E:W.23, E:Q.29, E:D.51, E:Y.56, E:K.84, E:S.154, E:S.154, E:R.155, E:S.210, E:L.212, E:C.214, E:S.218, E:K.220, E:R.230, E:R.230, E:R.230, E:L.288, E:S.291, E:S.291, E:Q.295, E:E.298, E:N.299 Water bridges: E:K.220, E:Y.228, E:G.289, E:G.289 Salt bridges: E:K.220, E:R.230, E:R.230 pi-Stacking: E:W.209 NAP.19: 33 residues within 4Å: Chain G: G.21, T.22, W.23, T.25, Q.29, D.51, Y.56, K.84, N.124, S.154, R.155, Q.180, W.209, S.210, P.211, L.212, A.213, C.214, G.215, S.218, K.220, Y.228, S.229, R.230, P.270, L.287, L.288, G.289, A.290, S.291, Q.295, E.298, N.299 33 PLIP interactions: 33 interactions with chain G Hydrophobic interactions: G:W.23, G:W.209 Hydrogen bonds: G:T.22, G:W.23, G:Q.29, G:D.51, G:Y.56, G:K.84, G:S.154, G:S.154, G:R.155, G:S.210, G:L.212, G:C.214, G:S.218, G:K.220, G:R.230, G:R.230, G:R.230, G:L.288, G:S.291, G:S.291, G:Q.295, G:E.298, G:N.299 Water bridges: G:K.220, G:Y.228, G:G.289, G:G.289 Salt bridges: G:K.220, G:R.230, G:R.230 pi-Stacking: G:W.209

16 x K: POTASSIUM ION(Non-covalent)

K.2: 15 residues within 4Å: Chain B: G.391, Y.392 Chain D: G.391, Y.392 Chain F: G.391, Y.392 Chain H: G.391, Y.392 Ligands: K.3, K.8, K.9, K.14, K.15, K.20, K.21 Ligand excluded by PLIP K.3: 19 residues within 4Å: Chain B: V.390, G.391 Chain D: V.390, G.391 Chain F: V.390, G.391 Chain H: V.390, G.391 Ligands: K.2, K.4, K.8, K.9, K.10, K.14, K.15, K.16, K.20, K.21, K.22 Ligand excluded by PLIP K.4: 19 residues within 4Å: Chain B: T.389, V.390 Chain D: T.389, V.390 Chain F: T.389, V.390 Chain H: T.389, V.390 Ligands: K.3, K.5, K.9, K.10, K.11, K.15, K.16, K.17, K.21, K.22, K.23 Ligand excluded by PLIP K.5: 11 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: K.4, K.10, K.11, K.16, K.17, K.22, K.23 Ligand excluded by PLIP K.8: 15 residues within 4Å: Chain B: G.391, Y.392 Chain D: G.391, Y.392 Chain F: G.391, Y.392 Chain H: G.391, Y.392 Ligands: K.2, K.3, K.9, K.14, K.15, K.20, K.21 Ligand excluded by PLIP K.9: 19 residues within 4Å: Chain B: V.390, G.391 Chain D: V.390, G.391 Chain F: V.390, G.391 Chain H: V.390, G.391 Ligands: K.2, K.3, K.4, K.8, K.10, K.14, K.15, K.16, K.20, K.21, K.22 Ligand excluded by PLIP K.10: 19 residues within 4Å: Chain B: T.389, V.390 Chain D: T.389, V.390 Chain F: T.389, V.390 Chain H: T.389, V.390 Ligands: K.3, K.4, K.5, K.9, K.11, K.15, K.16, K.17, K.21, K.22, K.23 Ligand excluded by PLIP K.11: 11 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: K.4, K.5, K.10, K.16, K.17, K.22, K.23 Ligand excluded by PLIP K.14: 15 residues within 4Å: Chain B: G.391, Y.392 Chain D: G.391, Y.392 Chain F: G.391, Y.392 Chain H: G.391, Y.392 Ligands: K.2, K.3, K.8, K.9, K.15, K.20, K.21 Ligand excluded by PLIP K.15: 19 residues within 4Å: Chain B: V.390, G.391 Chain D: V.390, G.391 Chain F: V.390, G.391 Chain H: V.390, G.391 Ligands: K.2, K.3, K.4, K.8, K.9, K.10, K.14, K.16, K.20, K.21, K.22 Ligand excluded by PLIP K.16: 19 residues within 4Å: Chain B: T.389, V.390 Chain D: T.389, V.390 Chain F: T.389, V.390 Chain H: T.389, V.390 Ligands: K.3, K.4, K.5, K.9, K.10, K.11, K.15, K.17, K.21, K.22, K.23 Ligand excluded by PLIP K.17: 11 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: K.4, K.5, K.10, K.11, K.16, K.22, K.23 Ligand excluded by PLIP K.20: 15 residues within 4Å: Chain B: G.391, Y.392 Chain D: G.391, Y.392 Chain F: G.391, Y.392 Chain H: G.391, Y.392 Ligands: K.2, K.3, K.8, K.9, K.14, K.15, K.21 Ligand excluded by PLIP K.21: 19 residues within 4Å: Chain B: V.390, G.391 Chain D: V.390, G.391 Chain F: V.390, G.391 Chain H: V.390, G.391 Ligands: K.2, K.3, K.4, K.8, K.9, K.10, K.14, K.15, K.16, K.20, K.22 Ligand excluded by PLIP K.22: 19 residues within 4Å: Chain B: T.389, V.390 Chain D: T.389, V.390 Chain F: T.389, V.390 Chain H: T.389, V.390 Ligands: K.3, K.4, K.5, K.9, K.10, K.11, K.15, K.16, K.17, K.21, K.23 Ligand excluded by PLIP K.23: 11 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: K.4, K.5, K.10, K.11, K.16, K.17, K.22 Ligand excluded by PLIP

4 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

PGW.6: 11 residues within 4Å: Chain B: P.377, D.378, F.380, W.381, V.384 Chain D: T.398, I.400, K.403, I.404, S.407 Chain F: L.201 7 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: D:K.403, D:I.404, B:F.380, B:W.381, F:L.201 Hydrogen bonds: D:T.398 Salt bridges: D:K.403 PGW.12: 11 residues within 4Å: Chain B: L.201 Chain D: P.377, D.378, F.380, W.381, V.384 Chain H: T.398, I.400, K.403, I.404, S.407 7 PLIP interactions: 2 interactions with chain D, 4 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: D:F.380, D:W.381, H:K.403, H:I.404, B:L.201 Hydrogen bonds: H:T.398 Salt bridges: H:K.403 PGW.18: 11 residues within 4Å: Chain B: T.398, I.400, K.403, I.404, S.407 Chain F: P.377, D.378, F.380, W.381, V.384 Chain H: L.201 7 PLIP interactions: 4 interactions with chain B, 1 interactions with chain H, 2 interactions with chain F Hydrophobic interactions: B:K.403, B:I.404, H:L.201, F:F.380, F:W.381 Hydrogen bonds: B:T.398 Salt bridges: B:K.403 PGW.24: 11 residues within 4Å: Chain D: L.201 Chain F: T.398, I.400, K.403, I.404, S.407 Chain H: P.377, D.378, F.380, W.381, V.384 7 PLIP interactions: 1 interactions with chain D, 4 interactions with chain F, 2 interactions with chain H Hydrophobic interactions: D:L.201, F:K.403, F:I.404, H:F.380, H:W.381 Hydrogen bonds: F:T.398 Salt bridges: F:K.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banerjee, A. et al., Structure of a pore-blocking toxin in complex with a eukaryotic voltage-dependent K(+) channel. Elife (2013)

Release Date

2013-06-12

Peptides

Voltage-gated potassium channel subunit beta-2: ACEG
Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1: BDFH
Potassium channel toxin alpha-KTx 1.1: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
G

E
G

G
G

B
H

D
H

F
H

H
H

I
Y

Membrane

We predict this structure to be a membrane protein.
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Voltage-gated potassium channel subunit beta-2

Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1

Potassium channel toxin alpha-KTx 1.1

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