SMTL ID : 4jta.2 (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-4-4-1-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, 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.221, 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: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:E.298, A:N.299 Water bridges: A:Q.29, A:N.124, A:R.230 Salt bridges: A:K.220, A:R.230 pi-Stacking: A:W.209 NAP.6: 33 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.221, 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: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:E.298, C:N.299 Water bridges: C:Q.29, C:N.124, C:R.230 Salt bridges: C:K.220, C:R.230 pi-Stacking: C:W.209 NAP.11: 33 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.221, 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: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:E.298, E:N.299 Water bridges: E:Q.29, E:N.124, E:R.230 Salt bridges: E:K.220, E:R.230 pi-Stacking: E:W.209 NAP.16: 33 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.221, 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: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:E.298, G:N.299 Water bridges: G:Q.29, G:N.124, G:R.230 Salt bridges: G:K.220, G:R.230 pi-Stacking: G:W.209

12 x K: POTASSIUM ION(Non-covalent)

K.2: 11 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.7, K.12, K.17 No protein-ligand interaction detected (PLIP) K.3: 15 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.4, K.8, K.9, K.13, K.14, K.18, K.19 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.8, K.9, K.13, K.14, K.18, K.19 No protein-ligand interaction detected (PLIP) K.7: 11 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.12, K.17 No protein-ligand interaction detected (PLIP) K.8: 15 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.9, K.13, K.14, K.18, K.19 No protein-ligand interaction detected (PLIP) K.9: 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.8, K.13, K.14, K.18, K.19 No protein-ligand interaction detected (PLIP) K.12: 11 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.7, K.17 No protein-ligand interaction detected (PLIP) K.13: 15 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.8, K.9, K.14, K.18, K.19 No protein-ligand interaction detected (PLIP) K.14: 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.8, K.9, K.13, K.18, K.19 No protein-ligand interaction detected (PLIP) K.17: 11 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.7, K.12 No protein-ligand interaction detected (PLIP) K.18: 15 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.8, K.9, K.13, K.14, K.19 No protein-ligand interaction detected (PLIP) K.19: 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.8, K.9, K.13, K.14, K.18 No protein-ligand interaction detected (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.5: 8 residues within 4Å: Chain B: I.347, P.377, F.380, W.381, V.384 Chain D: I.400, K.403, S.407 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:I.347, B:F.380, B:F.380 Hydrogen bonds: D:K.403 PGW.10: 8 residues within 4Å: Chain D: I.347, P.377, F.380, W.381, V.384 Chain H: I.400, K.403, S.407 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain D Hydrogen bonds: H:K.403 Hydrophobic interactions: D:I.347, D:F.380, D:F.380 PGW.15: 8 residues within 4Å: Chain B: I.400, K.403, S.407 Chain F: I.347, P.377, F.380, W.381, V.384 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:I.347, F:F.380, F:F.380 Hydrogen bonds: B:K.403 PGW.20: 8 residues within 4Å: Chain F: I.400, K.403, S.407 Chain H: I.347, P.377, F.380, W.381, V.384 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain F Hydrophobic interactions: H:I.347, H:F.380, H:F.380 Hydrogen bonds: 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
P

C
P

E
P

G
P

B
Q

D
Q

F
Q

H
Q

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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