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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

hetero-4-4-mer

Ligands

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

NAP.1: 31 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, 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 28 PLIP interactions: 28 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: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:G.289, A:S.291, A:S.291, A:Q.295, A:N.299, A:N.299 Salt bridges: A:K.220, A:R.230 pi-Stacking: A:W.209 NAP.22: 31 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, 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 28 PLIP interactions: 28 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: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:G.289, C:S.291, C:S.291, C:Q.295, C:N.299, C:N.299 Salt bridges: C:K.220, C:R.230 pi-Stacking: C:W.209 NAP.43: 31 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, 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 28 PLIP interactions: 28 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: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:G.289, E:S.291, E:S.291, E:Q.295, E:N.299, E:N.299 Salt bridges: E:K.220, E:R.230 pi-Stacking: E:W.209 NAP.64: 31 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, 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 28 PLIP interactions: 28 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: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:G.289, G:S.291, G:S.291, G:Q.295, G:N.299, G:N.299 Salt bridges: G:K.220, G:R.230 pi-Stacking: G:W.209

16 x CS: CESIUM ION(Non-covalent)(Non-functional Binders)

CS.2: 11 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: CS.23, CS.44, CS.65 Ligand excluded by PLIP CS.3: 11 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: CS.24, CS.45, CS.66 Ligand excluded by PLIP CS.4: 7 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: CS.25, CS.46, CS.67 Ligand excluded by PLIP CS.21: 3 residues within 4Å: Ligands: CS.42, CS.63, CS.84 Ligand excluded by PLIP CS.23: 11 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: CS.2, CS.44, CS.65 Ligand excluded by PLIP CS.24: 11 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: CS.3, CS.45, CS.66 Ligand excluded by PLIP CS.25: 7 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: CS.4, CS.46, CS.67 Ligand excluded by PLIP CS.42: 3 residues within 4Å: Ligands: CS.21, CS.63, CS.84 Ligand excluded by PLIP CS.44: 11 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: CS.2, CS.23, CS.65 Ligand excluded by PLIP CS.45: 11 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: CS.3, CS.24, CS.66 Ligand excluded by PLIP CS.46: 7 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: CS.4, CS.25, CS.67 Ligand excluded by PLIP CS.63: 3 residues within 4Å: Ligands: CS.21, CS.42, CS.84 Ligand excluded by PLIP CS.65: 11 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: CS.2, CS.23, CS.44 Ligand excluded by PLIP CS.66: 11 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: CS.3, CS.24, CS.45 Ligand excluded by PLIP CS.67: 7 residues within 4Å: Chain B: T.389 Chain D: T.389 Chain F: T.389 Chain H: T.389 Ligands: CS.4, CS.25, CS.46 Ligand excluded by PLIP CS.84: 3 residues within 4Å: Ligands: CS.21, CS.42, CS.63 Ligand excluded by 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: 11 residues within 4Å: Chain B: I.347, P.377, D.378, F.380, W.381, V.384 Chain H: I.400, K.403, S.407 Ligands: PGW.9, PGW.52 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain H Hydrophobic interactions: B:I.347, B:F.380, B:V.384 Hydrogen bonds: H:K.403 Salt bridges: H:K.403 PGW.6: 5 residues within 4Å: Chain B: I.313 Chain H: A.360, A.364 Ligands: PGW.7, PGW.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain H Hydrophobic interactions: B:I.313, H:A.360, H:A.364 PGW.7: 1 residues within 4Å: Ligands: PGW.6 No protein-ligand interaction detected (PLIP) PGW.8: 2 residues within 4Å: Chain B: L.317 Ligands: PGW.6 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.317 PGW.9: 1 residues within 4Å: Ligands: PGW.5 No protein-ligand interaction detected (PLIP) PGW.10: 3 residues within 4Å: Chain B: V.197 Chain H: P.377 Ligands: PGW.68 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:V.197, H:P.377 PGW.11: 6 residues within 4Å: Chain B: L.332, I.347 Chain H: A.412, T.416 Ligands: PGW.12, PGW.16 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:L.332, B:I.347, B:I.347, H:A.412 PGW.12: 4 residues within 4Å: Chain B: M.340, G.344 Ligands: PGW.11, PGW.57 No protein-ligand interaction detected (PLIP) PGW.13: 2 residues within 4Å: Chain B: I.206, F.207 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.206 PGW.14: 3 residues within 4Å: Chain B: I.194, P.240, F.241 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.194, B:P.240, B:F.241, B:F.241 PGW.15: 10 residues within 4Å: Chain B: L.322, H.325, S.326, K.327 Chain H: R.341, G.344, L.345, I.347, F.348 Ligands: PGW.75 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: H:I.347, H:F.348 Hydrogen bonds: H:R.341, B:K.327 PGW.16: 1 residues within 4Å: Ligands: PGW.11 No protein-ligand interaction detected (PLIP) 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 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.273, B:F.320, B:K.337 Hydrogen bonds: B:Q.334, B:R.434, B:R.434, B:R.434, B:E.435 PGW.18: 2 residues within 4Å: Chain B: F.242, Y.285 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.242 PGW.19: 3 residues within 4Å: Chain B: I.276, I.283, M.314 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.276 PGW.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGW.26: 11 residues within 4Å: Chain D: I.347, P.377, D.378, F.380, W.381, V.384 Chain F: I.400, K.403, S.407 Ligands: PGW.30, PGW.73 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:K.403 Salt bridges: F:K.403 Hydrophobic interactions: D:I.347, D:F.380, D:V.384 PGW.27: 5 residues within 4Å: Chain D: I.313 Chain F: A.360, A.364 Ligands: PGW.28, PGW.29 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:A.360, F:A.364, D:I.313 PGW.28: 1 residues within 4Å: Ligands: PGW.27 No protein-ligand interaction detected (PLIP) PGW.29: 2 residues within 4Å: Chain D: L.317 Ligands: PGW.27 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.317 PGW.30: 1 residues within 4Å: Ligands: PGW.26 No protein-ligand interaction detected (PLIP) PGW.31: 3 residues within 4Å: Chain D: V.197 Chain F: P.377 Ligands: PGW.47 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:V.197, F:P.377 PGW.32: 6 residues within 4Å: Chain D: L.332, I.347 Chain F: A.412, T.416 Ligands: PGW.33, PGW.37 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:L.332, D:I.347, D:I.347, F:A.412 PGW.33: 4 residues within 4Å: Chain D: M.340, G.344 Ligands: PGW.32, PGW.78 No protein-ligand interaction detected (PLIP) PGW.34: 2 residues within 4Å: Chain D: I.206, F.207 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.206 PGW.35: 3 residues within 4Å: Chain D: I.194, P.240, F.241 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.194, D:P.240, D:F.241, D:F.241 PGW.36: 10 residues within 4Å: Chain D: L.322, H.325, S.326, K.327 Chain F: R.341, G.344, L.345, I.347, F.348 Ligands: PGW.54 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:K.327, F:R.341 Hydrophobic interactions: F:I.347, F:F.348 PGW.37: 1 residues within 4Å: Ligands: PGW.32 No protein-ligand interaction detected (PLIP) PGW.38: 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 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.273, D:F.320, D:K.337 Hydrogen bonds: D:Q.334, D:R.434, D:R.434, D:R.434, D:E.435 PGW.39: 2 residues within 4Å: Chain D: F.242, Y.285 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.242 PGW.40: 3 residues within 4Å: Chain D: I.276, I.283, M.314 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.276 PGW.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGW.47: 11 residues within 4Å: Chain B: I.400, K.403, S.407 Chain F: I.347, P.377, D.378, F.380, W.381, V.384 Ligands: PGW.31, PGW.51 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:K.403 Salt bridges: B:K.403 Hydrophobic interactions: F:I.347, F:F.380, F:V.384 PGW.48: 5 residues within 4Å: Chain B: A.360, A.364 Chain F: I.313 Ligands: PGW.49, PGW.50 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:A.360, B:A.364, F:I.313 PGW.49: 1 residues within 4Å: Ligands: PGW.48 No protein-ligand interaction detected (PLIP) PGW.50: 2 residues within 4Å: Chain F: L.317 Ligands: PGW.48 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.317 PGW.51: 1 residues within 4Å: Ligands: PGW.47 No protein-ligand interaction detected (PLIP) PGW.52: 3 residues within 4Å: Chain B: P.377 Chain F: V.197 Ligands: PGW.5 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:V.197, B:P.377 PGW.53: 6 residues within 4Å: Chain B: A.412, T.416 Chain F: L.332, I.347 Ligands: PGW.54, PGW.58 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:L.332, F:I.347, F:I.347, B:A.412 PGW.54: 4 residues within 4Å: Chain F: M.340, G.344 Ligands: PGW.36, PGW.53 No protein-ligand interaction detected (PLIP) PGW.55: 2 residues within 4Å: Chain F: I.206, F.207 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.206 PGW.56: 3 residues within 4Å: Chain F: I.194, P.240, F.241 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:I.194, F:P.240, F:F.241, F:F.241 PGW.57: 10 residues within 4Å: Chain B: R.341, G.344, L.345, I.347, F.348 Chain F: L.322, H.325, S.326, K.327 Ligands: PGW.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:I.347, B:F.348 Hydrogen bonds: B:R.341, F:K.327 PGW.58: 1 residues within 4Å: Ligands: PGW.53 No protein-ligand interaction detected (PLIP) PGW.59: 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 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.273, F:F.320, F:K.337 Hydrogen bonds: F:Q.334, F:R.434, F:R.434, F:R.434, F:E.435 PGW.60: 2 residues within 4Å: Chain F: F.242, Y.285 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.242 PGW.61: 3 residues within 4Å: Chain F: I.276, I.283, M.314 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.276 PGW.62: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGW.68: 11 residues within 4Å: Chain D: I.400, K.403, S.407 Chain H: I.347, P.377, D.378, F.380, W.381, V.384 Ligands: PGW.10, PGW.72 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:I.347, H:F.380, H:V.384 Hydrogen bonds: D:K.403 Salt bridges: D:K.403 PGW.69: 5 residues within 4Å: Chain D: A.360, A.364 Chain H: I.313 Ligands: PGW.70, PGW.71 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain H Hydrophobic interactions: D:A.360, D:A.364, H:I.313 PGW.70: 1 residues within 4Å: Ligands: PGW.69 No protein-ligand interaction detected (PLIP) PGW.71: 2 residues within 4Å: Chain H: L.317 Ligands: PGW.69 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:L.317 PGW.72: 1 residues within 4Å: Ligands: PGW.68 No protein-ligand interaction detected (PLIP) PGW.73: 3 residues within 4Å: Chain D: P.377 Chain H: V.197 Ligands: PGW.26 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain D Hydrophobic interactions: H:V.197, D:P.377 PGW.74: 6 residues within 4Å: Chain D: A.412, T.416 Chain H: L.332, I.347 Ligands: PGW.75, PGW.79 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain D Hydrophobic interactions: H:L.332, H:I.347, H:I.347, D:A.412 PGW.75: 4 residues within 4Å: Chain H: M.340, G.344 Ligands: PGW.15, PGW.74 No protein-ligand interaction detected (PLIP) PGW.76: 2 residues within 4Å: Chain H: I.206, F.207 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:I.206 PGW.77: 3 residues within 4Å: Chain H: I.194, P.240, F.241 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:I.194, H:P.240, H:F.241, H:F.241 PGW.78: 10 residues within 4Å: Chain D: R.341, G.344, L.345, I.347, F.348 Chain H: L.322, H.325, S.326, K.327 Ligands: PGW.33 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain H Hydrophobic interactions: D:I.347, D:F.348 Hydrogen bonds: D:R.341, H:K.327 PGW.79: 1 residues within 4Å: Ligands: PGW.74 No protein-ligand interaction detected (PLIP) PGW.80: 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 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:I.273, H:F.320, H:K.337 Hydrogen bonds: H:Q.334, H:R.434, H:R.434, H:R.434, H:E.435 PGW.81: 2 residues within 4Å: Chain H: F.242, Y.285 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:F.242 PGW.82: 3 residues within 4Å: Chain H: I.276, I.283, M.314 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:I.276 PGW.83: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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.
Show / Hide

Voltage-gated potassium channel subunit beta-2

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

Related Entries With Identical Sequence