SMTL ID : 7rp0.1

Structural Snapshots of Intermediates in the Gating of a K+ Channel

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x F09: NONAN-1-OL(Non-covalent)

F09.1: 5 residues within 4Å: Chain A: R.57 Chain C: L.25, L.28, W.66, V.70 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.25, C:L.25, C:W.66, C:W.66, C:V.70 Hydrogen bonds: A:R.57 F09.8: 5 residues within 4Å: Chain D: R.57 Chain F: L.25, L.28, W.66, V.70 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:L.25, F:L.25, F:W.66, F:W.66, F:V.70 Hydrogen bonds: D:R.57 F09.15: 5 residues within 4Å: Chain G: R.57 Chain I: L.25, L.28, W.66, V.70 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: I:L.25, I:L.25, I:W.66, I:W.66, I:V.70 Hydrogen bonds: G:R.57 F09.22: 5 residues within 4Å: Chain J: R.57 Chain L: L.25, L.28, W.66, V.70 6 PLIP interactions: 5 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: L:L.25, L:L.25, L:W.66, L:W.66, L:V.70 Hydrogen bonds: J:R.57

16 x K: POTASSIUM ION(Non-covalent)

K.2: 15 residues within 4Å: Chain C: G.56, Y.57 Chain F: G.56, Y.57 Chain I: G.56, Y.57 Chain L: G.56, Y.57 Ligands: K.3, K.9, K.10, K.16, K.17, K.23, K.24 Ligand excluded by PLIP K.3: 19 residues within 4Å: Chain C: V.55, G.56 Chain F: V.55, G.56 Chain I: V.55, G.56 Chain L: V.55, G.56 Ligands: K.2, K.4, K.9, K.10, K.11, K.16, K.17, K.18, K.23, K.24, K.25 Ligand excluded by PLIP K.4: 19 residues within 4Å: Chain C: T.54, V.55 Chain F: T.54, V.55 Chain I: T.54, V.55 Chain L: T.54, V.55 Ligands: K.3, K.5, K.10, K.11, K.12, K.17, K.18, K.19, K.24, K.25, K.26 Ligand excluded by PLIP K.5: 11 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: K.4, K.11, K.12, K.18, K.19, K.25, K.26 Ligand excluded by PLIP K.9: 15 residues within 4Å: Chain C: G.56, Y.57 Chain F: G.56, Y.57 Chain I: G.56, Y.57 Chain L: G.56, Y.57 Ligands: K.2, K.3, K.10, K.16, K.17, K.23, K.24 Ligand excluded by PLIP K.10: 19 residues within 4Å: Chain C: V.55, G.56 Chain F: V.55, G.56 Chain I: V.55, G.56 Chain L: V.55, G.56 Ligands: K.2, K.3, K.4, K.9, K.11, K.16, K.17, K.18, K.23, K.24, K.25 Ligand excluded by PLIP K.11: 19 residues within 4Å: Chain C: T.54, V.55 Chain F: T.54, V.55 Chain I: T.54, V.55 Chain L: T.54, V.55 Ligands: K.3, K.4, K.5, K.10, K.12, K.17, K.18, K.19, K.24, K.25, K.26 Ligand excluded by PLIP K.12: 11 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: K.4, K.5, K.11, K.18, K.19, K.25, K.26 Ligand excluded by PLIP K.16: 15 residues within 4Å: Chain C: G.56, Y.57 Chain F: G.56, Y.57 Chain I: G.56, Y.57 Chain L: G.56, Y.57 Ligands: K.2, K.3, K.9, K.10, K.17, K.23, K.24 Ligand excluded by PLIP K.17: 19 residues within 4Å: Chain C: V.55, G.56 Chain F: V.55, G.56 Chain I: V.55, G.56 Chain L: V.55, G.56 Ligands: K.2, K.3, K.4, K.9, K.10, K.11, K.16, K.18, K.23, K.24, K.25 Ligand excluded by PLIP K.18: 19 residues within 4Å: Chain C: T.54, V.55 Chain F: T.54, V.55 Chain I: T.54, V.55 Chain L: T.54, V.55 Ligands: K.3, K.4, K.5, K.10, K.11, K.12, K.17, K.19, K.24, K.25, K.26 Ligand excluded by PLIP K.19: 11 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: K.4, K.5, K.11, K.12, K.18, K.25, K.26 Ligand excluded by PLIP K.23: 15 residues within 4Å: Chain C: G.56, Y.57 Chain F: G.56, Y.57 Chain I: G.56, Y.57 Chain L: G.56, Y.57 Ligands: K.2, K.3, K.9, K.10, K.16, K.17, K.24 Ligand excluded by PLIP K.24: 19 residues within 4Å: Chain C: V.55, G.56 Chain F: V.55, G.56 Chain I: V.55, G.56 Chain L: V.55, G.56 Ligands: K.2, K.3, K.4, K.9, K.10, K.11, K.16, K.17, K.18, K.23, K.25 Ligand excluded by PLIP K.25: 19 residues within 4Å: Chain C: T.54, V.55 Chain F: T.54, V.55 Chain I: T.54, V.55 Chain L: T.54, V.55 Ligands: K.3, K.4, K.5, K.10, K.11, K.12, K.17, K.18, K.19, K.24, K.26 Ligand excluded by PLIP K.26: 11 residues within 4Å: Chain C: T.54 Chain F: T.54 Chain I: T.54 Chain L: T.54 Ligands: K.4, K.5, K.11, K.12, K.18, K.19, K.25 Ligand excluded by PLIP

4 x TBA: TETRABUTYLAMMONIUM ION(Non-covalent)

TBA.6: 21 residues within 4Å: Chain C: T.54, I.79 Chain F: A.52, T.53, T.54, G.78, I.79, F.82 Chain I: T.53, T.54, I.79, F.82 Chain L: A.52, T.53, T.54, G.78, I.79, F.82 Ligands: TBA.13, TBA.20, TBA.27 12 PLIP interactions: 3 interactions with chain L, 4 interactions with chain I, 3 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: L:T.54, L:I.79, L:F.82, I:T.54, I:I.79, I:I.79, I:F.82, C:T.54, C:I.79, C:I.79, F:I.79, F:F.82 TBA.13: 21 residues within 4Å: Chain C: A.52, T.53, T.54, G.78, I.79, F.82 Chain F: T.54, I.79 Chain I: A.52, T.53, T.54, G.78, I.79, F.82 Chain L: T.53, T.54, I.79, F.82 Ligands: TBA.6, TBA.20, TBA.27 12 PLIP interactions: 3 interactions with chain F, 4 interactions with chain L, 3 interactions with chain I, 2 interactions with chain C Hydrophobic interactions: F:T.54, F:I.79, F:I.79, L:T.54, L:I.79, L:I.79, L:F.82, I:T.54, I:I.79, I:F.82, C:I.79, C:F.82 TBA.20: 21 residues within 4Å: Chain C: A.52, T.53, T.54, G.78, I.79, F.82 Chain F: T.53, T.54, I.79, F.82 Chain I: T.54, I.79 Chain L: A.52, T.53, T.54, G.78, I.79, F.82 Ligands: TBA.6, TBA.13, TBA.27 12 PLIP interactions: 4 interactions with chain F, 2 interactions with chain L, 3 interactions with chain I, 3 interactions with chain C Hydrophobic interactions: F:T.54, F:I.79, F:I.79, F:F.82, L:I.79, L:F.82, I:T.54, I:I.79, I:I.79, C:T.54, C:I.79, C:F.82 TBA.27: 21 residues within 4Å: Chain C: T.53, T.54, I.79, F.82 Chain F: A.52, T.53, T.54, G.78, I.79, F.82 Chain I: A.52, T.53, T.54, G.78, I.79, F.82 Chain L: T.54, I.79 Ligands: TBA.6, TBA.13, TBA.20 12 PLIP interactions: 3 interactions with chain F, 3 interactions with chain L, 2 interactions with chain I, 4 interactions with chain C Hydrophobic interactions: F:T.54, F:I.79, F:F.82, L:T.54, L:I.79, L:I.79, I:I.79, I:F.82, C:T.54, C:I.79, C:I.79, C:F.82

4 x DGA: DIACYL GLYCEROL(Non-covalent)

DGA.7: 10 residues within 4Å: Chain C: L.65, R.68, L.69, V.72 Chain I: L.20, S.23, Y.24, P.42, W.46, V.49 8 PLIP interactions: 4 interactions with chain I, 4 interactions with chain C Hydrophobic interactions: I:L.20, I:Y.24, I:Y.24, I:W.46, C:L.65, C:L.65, C:V.72 Salt bridges: C:R.68 DGA.14: 10 residues within 4Å: Chain F: L.65, R.68, L.69, V.72 Chain L: L.20, S.23, Y.24, P.42, W.46, V.49 8 PLIP interactions: 4 interactions with chain L, 4 interactions with chain F Hydrophobic interactions: L:L.20, L:Y.24, L:Y.24, L:W.46, F:L.65, F:L.65, F:V.72 Salt bridges: F:R.68 DGA.21: 10 residues within 4Å: Chain F: L.20, S.23, Y.24, P.42, W.46, V.49 Chain I: L.65, R.68, L.69, V.72 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain I Hydrophobic interactions: F:L.20, F:Y.24, F:Y.24, F:W.46, I:L.65, I:L.65, I:V.72 Salt bridges: I:R.68 DGA.28: 10 residues within 4Å: Chain C: L.20, S.23, Y.24, P.42, W.46, V.49 Chain L: L.65, R.68, L.69, V.72 8 PLIP interactions: 4 interactions with chain L, 4 interactions with chain C Hydrophobic interactions: L:L.65, L:L.65, L:V.72, C:L.20, C:Y.24, C:Y.24, C:W.46 Salt bridges: L:R.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reddi, R. et al., Structures of Gating Intermediates in a K + channell. J.Mol.Biol. (2021)

Release Date

2021-10-27

Peptides

KcsA Fab chain A: ADGJ
KcsA Fab chain B: BEHK
pH-gated potassium channel KcsA: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
B

E
B

H
B

K
B

C
C

F
C

I
C

L
C

Membrane

We predict this structure to be a membrane protein.
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KcsA Fab chain A

KcsA Fab chain B

pH-gated potassium channel KcsA

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