SMTL ID : 4jta.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-4-4-mer

Ligands

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

NAP.1: 32 residues within 4Å: Chain A: G.21, T.22, W.23, 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 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:T.22, A:W.23, A:Q.29, A:D.51, A:S.154, A:S.154, A:R.155, A:S.210, A:L.212, A:C.214, A:G.215, A:S.218, A:K.220, A:R.230, A:R.230, A:G.289, A:S.291, A:Q.295, A:Q.295, A:N.299, A:N.299 Water bridges: A:K.84 Salt bridges: A:K.220, A:R.230 pi-Stacking: A:W.209, A:W.209 NAP.21: 32 residues within 4Å: Chain C: G.21, T.22, W.23, 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 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:W.23 Hydrogen bonds: C:T.22, C:W.23, C:Q.29, C:D.51, C:S.154, C:S.154, C:R.155, C:S.210, C:L.212, C:C.214, C:G.215, C:S.218, C:K.220, C:R.230, C:R.230, C:G.289, C:S.291, C:Q.295, C:Q.295, C:N.299, C:N.299 Water bridges: C:K.84 Salt bridges: C:K.220, C:R.230 pi-Stacking: C:W.209, C:W.209 NAP.41: 32 residues within 4Å: Chain E: G.21, T.22, W.23, 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 27 PLIP interactions: 27 interactions with chain E Hydrophobic interactions: E:W.23 Hydrogen bonds: E:T.22, E:W.23, E:Q.29, E:D.51, E:S.154, E:S.154, E:R.155, E:S.210, E:L.212, E:C.214, E:G.215, E:S.218, E:K.220, E:R.230, E:R.230, E:G.289, E:S.291, E:Q.295, E:Q.295, E:N.299, E:N.299 Water bridges: E:K.84 Salt bridges: E:K.220, E:R.230 pi-Stacking: E:W.209, E:W.209 NAP.61: 32 residues within 4Å: Chain G: G.21, T.22, W.23, 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 27 PLIP interactions: 27 interactions with chain G Hydrophobic interactions: G:W.23 Hydrogen bonds: G:T.22, G:W.23, G:Q.29, G:D.51, G:S.154, G:S.154, G:R.155, G:S.210, G:L.212, G:C.214, G:G.215, G:S.218, G:K.220, G:R.230, G:R.230, G:G.289, G:S.291, G:Q.295, G:Q.295, G:N.299, G:N.299 Water bridges: G:K.84 Salt bridges: G:K.220, G:R.230 pi-Stacking: G:W.209, G:W.209

12 x K: POTASSIUM ION(Non-covalent)

K.2: 15 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.3, K.22, K.23, K.42, K.43, K.62, K.63 No protein-ligand interaction detected (PLIP) K.3: 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.2, K.4, K.22, K.23, K.24, K.42, K.43, K.44, K.62, K.63, K.64 No protein-ligand interaction detected (PLIP) K.4: 11 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: K.3, K.23, K.24, K.43, K.44, K.63, K.64 No protein-ligand interaction detected (PLIP) K.22: 15 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.23, K.42, K.43, K.62, K.63 No protein-ligand interaction detected (PLIP) K.23: 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.2, K.3, K.4, K.22, K.24, K.42, K.43, K.44, K.62, K.63, K.64 No protein-ligand interaction detected (PLIP) K.24: 11 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: K.3, K.4, K.23, K.43, K.44, K.63, K.64 No protein-ligand interaction detected (PLIP) K.42: 15 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.22, K.23, K.43, K.62, K.63 No protein-ligand interaction detected (PLIP) K.43: 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.2, K.3, K.4, K.22, K.23, K.24, K.42, K.44, K.62, K.63, K.64 No protein-ligand interaction detected (PLIP) K.44: 11 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: K.3, K.4, K.23, K.24, K.43, K.63, K.64 No protein-ligand interaction detected (PLIP) K.62: 15 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.22, K.23, K.42, K.43, K.63 No protein-ligand interaction detected (PLIP) K.63: 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.2, K.3, K.4, K.22, K.23, K.24, K.42, K.43, K.44, K.62, K.64 No protein-ligand interaction detected (PLIP) K.64: 11 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: K.3, K.4, K.23, K.24, K.43, K.44, K.63 No protein-ligand interaction detected (PLIP)

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

PGW.5: 9 residues within 4Å: Chain B: P.377, D.378, F.380, W.381, V.384 Chain H: I.400, K.403, S.407 Ligands: PGW.50 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain H Hydrophobic interactions: B:F.380, B:W.381, B:V.384 Hydrogen bonds: H:K.403, H:K.403 Salt bridges: H:K.403 PGW.6: 4 residues within 4Å: Chain B: I.313 Chain H: F.363, A.364 Ligands: PGW.7 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: H:A.364, B:I.313 PGW.7: 3 residues within 4Å: Chain H: I.404 Ligands: PGW.6, PGW.9 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:I.404 PGW.8: 3 residues within 4Å: Chain B: I.310, M.314, L.317 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.310, B:M.314, B:L.317 PGW.9: 2 residues within 4Å: Chain H: I.404 Ligands: PGW.7 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:I.404 PGW.10: 5 residues within 4Å: Chain B: V.197, L.201, L.204 Chain H: P.377 Ligands: PGW.65 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:V.197, B:L.201, B:L.204, H:P.377 PGW.11: 6 residues within 4Å: Chain B: L.332, I.347 Chain H: L.415, T.416 Ligands: PGW.12, PGW.16 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain H Hydrophobic interactions: B:L.332, B:I.347, H:L.415, H:L.415 PGW.12: 3 residues within 4Å: Chain B: M.340, G.344 Ligands: PGW.11 No protein-ligand interaction detected (PLIP) PGW.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGW.14: 2 residues within 4Å: Chain B: P.240, F.241 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.240, B:P.240, B:F.241, B:F.241 PGW.15: 11 residues within 4Å: Chain B: V.189, L.193, H.325, S.326, K.327, G.328 Chain H: R.341, G.344, L.345, I.347, F.348 7 PLIP interactions: 3 interactions with chain H, 4 interactions with chain B Hydrophobic interactions: H:I.347, H:F.348, B:V.189, B:L.193 Salt bridges: H:R.341 Hydrogen bonds: B:K.327, B:G.328 PGW.16: 4 residues within 4Å: Chain H: F.349, I.352, T.416 Ligands: PGW.11 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:F.349, H:I.352 PGW.17: 11 residues within 4Å: Chain B: I.273, M.274, F.320, K.327, L.329, Q.330, G.333, Q.334, K.337, R.434, E.435 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.273, B:F.320, B:Q.330, B:K.337, B:K.337 Hydrogen bonds: B:Q.334, B:R.434, B:R.434, B:R.434 Salt bridges: B:K.327 PGW.18: 5 residues within 4Å: Chain B: Q.233, S.234, T.235, I.250, E.293 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.250 PGW.19: 3 residues within 4Å: Chain B: I.276, I.283, F.311 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.276, B:I.283, B:F.311, B:F.311 PGW.20: 1 residues within 4Å: Chain B: F.237 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.237 PGW.25: 9 residues within 4Å: Chain D: P.377, D.378, F.380, W.381, V.384 Chain F: I.400, K.403, S.407 Ligands: PGW.70 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:K.403, F:K.403 Salt bridges: F:K.403 Hydrophobic interactions: D:F.380, D:W.381, D:V.384 PGW.26: 4 residues within 4Å: Chain D: I.313 Chain F: F.363, A.364 Ligands: PGW.27 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:A.364, D:I.313 PGW.27: 3 residues within 4Å: Chain F: I.404 Ligands: PGW.26, PGW.29 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.404 PGW.28: 3 residues within 4Å: Chain D: I.310, M.314, L.317 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.310, D:M.314, D:L.317 PGW.29: 2 residues within 4Å: Chain F: I.404 Ligands: PGW.27 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.404 PGW.30: 5 residues within 4Å: Chain D: V.197, L.201, L.204 Chain F: P.377 Ligands: PGW.45 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:V.197, D:L.201, D:L.204, F:P.377 PGW.31: 6 residues within 4Å: Chain D: L.332, I.347 Chain F: L.415, T.416 Ligands: PGW.32, PGW.36 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:L.415, F:L.415, D:L.332, D:I.347 PGW.32: 3 residues within 4Å: Chain D: M.340, G.344 Ligands: PGW.31 No protein-ligand interaction detected (PLIP) PGW.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGW.34: 2 residues within 4Å: Chain D: P.240, F.241 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.240, D:P.240, D:F.241, D:F.241 PGW.35: 11 residues within 4Å: Chain D: V.189, L.193, H.325, S.326, K.327, G.328 Chain F: R.341, G.344, L.345, I.347, F.348 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: F:I.347, F:F.348, D:V.189, D:L.193 Salt bridges: F:R.341 Hydrogen bonds: D:K.327, D:G.328 PGW.36: 4 residues within 4Å: Chain F: F.349, I.352, T.416 Ligands: PGW.31 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.349, F:I.352 PGW.37: 11 residues within 4Å: Chain D: I.273, M.274, F.320, K.327, L.329, Q.330, G.333, Q.334, K.337, R.434, E.435 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.273, D:F.320, D:Q.330, D:K.337, D:K.337 Hydrogen bonds: D:Q.334, D:R.434, D:R.434, D:R.434 Salt bridges: D:K.327 PGW.38: 5 residues within 4Å: Chain D: Q.233, S.234, T.235, I.250, E.293 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.250 PGW.39: 3 residues within 4Å: Chain D: I.276, I.283, F.311 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.276, D:I.283, D:F.311, D:F.311 PGW.40: 1 residues within 4Å: Chain D: F.237 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.237 PGW.45: 9 residues within 4Å: Chain B: I.400, K.403, S.407 Chain F: P.377, D.378, F.380, W.381, V.384 Ligands: PGW.30 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:F.380, F:W.381, F:V.384 Hydrogen bonds: B:K.403, B:K.403 Salt bridges: B:K.403 PGW.46: 4 residues within 4Å: Chain B: F.363, A.364 Chain F: I.313 Ligands: PGW.47 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:A.364, F:I.313 PGW.47: 3 residues within 4Å: Chain B: I.404 Ligands: PGW.46, PGW.49 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.404 PGW.48: 3 residues within 4Å: Chain F: I.310, M.314, L.317 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:I.310, F:M.314, F:L.317 PGW.49: 2 residues within 4Å: Chain B: I.404 Ligands: PGW.47 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.404 PGW.50: 5 residues within 4Å: Chain B: P.377 Chain F: V.197, L.201, L.204 Ligands: PGW.5 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:V.197, F:L.201, F:L.204, B:P.377 PGW.51: 6 residues within 4Å: Chain B: L.415, T.416 Chain F: L.332, I.347 Ligands: PGW.52, PGW.56 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:L.332, F:I.347, B:L.415, B:L.415 PGW.52: 3 residues within 4Å: Chain F: M.340, G.344 Ligands: PGW.51 No protein-ligand interaction detected (PLIP) PGW.53: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGW.54: 2 residues within 4Å: Chain F: P.240, F.241 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:P.240, F:P.240, F:F.241, F:F.241 PGW.55: 11 residues within 4Å: Chain B: R.341, G.344, L.345, I.347, F.348 Chain F: V.189, L.193, H.325, S.326, K.327, G.328 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:V.189, F:L.193, B:I.347, B:F.348 Hydrogen bonds: F:K.327, F:G.328 Salt bridges: B:R.341 PGW.56: 4 residues within 4Å: Chain B: F.349, I.352, T.416 Ligands: PGW.51 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.349, B:I.352 PGW.57: 11 residues within 4Å: Chain F: I.273, M.274, F.320, K.327, L.329, Q.330, G.333, Q.334, K.337, R.434, E.435 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:I.273, F:F.320, F:Q.330, F:K.337, F:K.337 Hydrogen bonds: F:Q.334, F:R.434, F:R.434, F:R.434 Salt bridges: F:K.327 PGW.58: 5 residues within 4Å: Chain F: Q.233, S.234, T.235, I.250, E.293 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.250 PGW.59: 3 residues within 4Å: Chain F: I.276, I.283, F.311 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:I.276, F:I.283, F:F.311, F:F.311 PGW.60: 1 residues within 4Å: Chain F: F.237 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.237 PGW.65: 9 residues within 4Å: Chain D: I.400, K.403, S.407 Chain H: P.377, D.378, F.380, W.381, V.384 Ligands: PGW.10 6 PLIP interactions: 3 interactions with chain H, 3 interactions with chain D Hydrophobic interactions: H:F.380, H:W.381, H:V.384 Hydrogen bonds: D:K.403, D:K.403 Salt bridges: D:K.403 PGW.66: 4 residues within 4Å: Chain D: F.363, A.364 Chain H: I.313 Ligands: PGW.67 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain D Hydrophobic interactions: H:I.313, D:A.364 PGW.67: 3 residues within 4Å: Chain D: I.404 Ligands: PGW.66, PGW.69 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.404 PGW.68: 3 residues within 4Å: Chain H: I.310, M.314, L.317 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:I.310, H:M.314, H:L.317 PGW.69: 2 residues within 4Å: Chain D: I.404 Ligands: PGW.67 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.404 PGW.70: 5 residues within 4Å: Chain D: P.377 Chain H: V.197, L.201, L.204 Ligands: PGW.25 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain D Hydrophobic interactions: H:V.197, H:L.201, H:L.204, D:P.377 PGW.71: 6 residues within 4Å: Chain D: L.415, T.416 Chain H: L.332, I.347 Ligands: PGW.72, PGW.76 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:L.332, H:I.347, D:L.415, D:L.415 PGW.72: 3 residues within 4Å: Chain H: M.340, G.344 Ligands: PGW.71 No protein-ligand interaction detected (PLIP) PGW.73: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGW.74: 2 residues within 4Å: Chain H: P.240, F.241 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:P.240, H:P.240, H:F.241, H:F.241 PGW.75: 11 residues within 4Å: Chain D: R.341, G.344, L.345, I.347, F.348 Chain H: V.189, L.193, H.325, S.326, K.327, G.328 7 PLIP interactions: 4 interactions with chain H, 3 interactions with chain D Hydrophobic interactions: H:V.189, H:L.193, D:I.347, D:F.348 Hydrogen bonds: H:K.327, H:G.328 Salt bridges: D:R.341 PGW.76: 4 residues within 4Å: Chain D: F.349, I.352, T.416 Ligands: PGW.71 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.349, D:I.352 PGW.77: 11 residues within 4Å: Chain H: I.273, M.274, F.320, K.327, L.329, Q.330, G.333, Q.334, K.337, R.434, E.435 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:I.273, H:F.320, H:Q.330, H:K.337, H:K.337 Hydrogen bonds: H:Q.334, H:R.434, H:R.434, H:R.434 Salt bridges: H:K.327 PGW.78: 5 residues within 4Å: Chain H: Q.233, S.234, T.235, I.250, E.293 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:I.250 PGW.79: 3 residues within 4Å: Chain H: I.276, I.283, F.311 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:I.276, H:I.283, H:F.311, H:F.311 PGW.80: 1 residues within 4Å: Chain H: F.237 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:F.237

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

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

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