SMTL ID : 7m2h.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

hetero-4-4-4-mer

Ligands

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

F09.1: 6 residues within 4Å: Chain A: Y.55, R.57 Chain C: L.46, L.49, A.50, W.87 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.46, C:L.49, C:W.87 Hydrogen bonds: A:R.57 F09.10: 6 residues within 4Å: Chain D: Y.55, R.57 Chain F: L.46, L.49, A.50, W.87 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:L.46, F:L.49, F:W.87 Hydrogen bonds: D:R.57 F09.19: 6 residues within 4Å: Chain G: Y.55, R.57 Chain I: L.46, L.49, A.50, W.87 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: I:L.46, I:L.49, I:W.87 Hydrogen bonds: G:R.57 F09.28: 6 residues within 4Å: Chain J: Y.55, R.57 Chain L: L.46, L.49, A.50, W.87 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain L Hydrogen bonds: J:R.57 Hydrophobic interactions: L:L.46, L:L.49, L:W.87

4 x TBA: TETRABUTYLAMMONIUM ION(Non-covalent)

TBA.2: 23 residues within 4Å: Chain C: T.74, T.75, G.99, F.103 Chain F: T.74, T.75, F.103 Chain I: A.73, T.75, G.99, F.103 Chain L: A.73, T.75, G.99, I.100, F.103 Ligands: K.4, TBA.11, K.13, TBA.20, K.22, TBA.29, K.31 6 PLIP interactions: 1 interactions with chain F, 1 interactions with chain I, 2 interactions with chain C, 2 interactions with chain L Hydrophobic interactions: F:F.103, I:F.103, C:T.75, C:F.103, L:I.100, L:F.103 TBA.11: 23 residues within 4Å: Chain C: T.74, T.75, F.103 Chain F: T.74, T.75, G.99, F.103 Chain I: A.73, T.75, G.99, I.100, F.103 Chain L: A.73, T.75, G.99, F.103 Ligands: TBA.2, K.4, K.13, TBA.20, K.22, TBA.29, K.31 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain I, 1 interactions with chain C, 1 interactions with chain L Hydrophobic interactions: F:T.75, F:F.103, I:I.100, I:F.103, C:F.103, L:F.103 TBA.20: 23 residues within 4Å: Chain C: A.73, T.75, G.99, I.100, F.103 Chain F: A.73, T.75, G.99, F.103 Chain I: T.74, T.75, G.99, F.103 Chain L: T.74, T.75, F.103 Ligands: TBA.2, K.4, TBA.11, K.13, K.22, TBA.29, K.31 6 PLIP interactions: 1 interactions with chain F, 2 interactions with chain I, 2 interactions with chain C, 1 interactions with chain L Hydrophobic interactions: F:F.103, I:T.75, I:F.103, C:I.100, C:F.103, L:F.103 TBA.29: 23 residues within 4Å: Chain C: A.73, T.75, G.99, F.103 Chain F: A.73, T.75, G.99, I.100, F.103 Chain I: T.74, T.75, F.103 Chain L: T.74, T.75, G.99, F.103 Ligands: TBA.2, K.4, TBA.11, K.13, TBA.20, K.22, K.31 6 PLIP interactions: 2 interactions with chain F, 1 interactions with chain I, 1 interactions with chain C, 2 interactions with chain L Hydrophobic interactions: F:I.100, F:F.103, I:F.103, C:F.103, L:T.75, L:F.103

24 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.3: 19 residues within 4Å: Chain C: T.75, V.76 Chain F: T.75, V.76 Chain I: T.75, V.76 Chain L: T.75, V.76 Ligands: K.4, K.5, K.12, K.13, K.14, K.21, K.22, K.23, K.30, K.31, K.32 Ligand excluded by PLIP K.4: 15 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: TBA.2, K.3, TBA.11, K.12, K.13, TBA.20, K.21, K.22, TBA.29, K.30, K.31 Ligand excluded by PLIP K.5: 19 residues within 4Å: Chain C: V.76, G.77 Chain F: V.76, G.77 Chain I: V.76, G.77 Chain L: V.76, G.77 Ligands: K.3, K.8, K.12, K.14, K.17, K.21, K.23, K.26, K.30, K.32, K.35 Ligand excluded by PLIP K.6: 15 residues within 4Å: Chain C: Y.78 Chain F: Y.78 Chain I: Y.78 Chain L: Y.78 Ligands: K.7, K.8, K.15, K.16, K.17, K.24, K.25, K.26, K.33, K.34, K.35 Ligand excluded by PLIP K.7: 7 residues within 4Å: Ligands: K.6, K.15, K.16, K.24, K.25, K.33, K.34 Ligand excluded by PLIP K.8: 19 residues within 4Å: Chain C: G.77, Y.78 Chain F: G.77, Y.78 Chain I: G.77, Y.78 Chain L: G.77, Y.78 Ligands: K.5, K.6, K.14, K.15, K.17, K.23, K.24, K.26, K.32, K.33, K.35 Ligand excluded by PLIP K.12: 19 residues within 4Å: Chain C: T.75, V.76 Chain F: T.75, V.76 Chain I: T.75, V.76 Chain L: T.75, V.76 Ligands: K.3, K.4, K.5, K.13, K.14, K.21, K.22, K.23, K.30, K.31, K.32 Ligand excluded by PLIP K.13: 15 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: TBA.2, K.3, K.4, TBA.11, K.12, TBA.20, K.21, K.22, TBA.29, K.30, K.31 Ligand excluded by PLIP K.14: 19 residues within 4Å: Chain C: V.76, G.77 Chain F: V.76, G.77 Chain I: V.76, G.77 Chain L: V.76, G.77 Ligands: K.3, K.5, K.8, K.12, K.17, K.21, K.23, K.26, K.30, K.32, K.35 Ligand excluded by PLIP K.15: 15 residues within 4Å: Chain C: Y.78 Chain F: Y.78 Chain I: Y.78 Chain L: Y.78 Ligands: K.6, K.7, K.8, K.16, K.17, K.24, K.25, K.26, K.33, K.34, K.35 Ligand excluded by PLIP K.16: 7 residues within 4Å: Ligands: K.6, K.7, K.15, K.24, K.25, K.33, K.34 Ligand excluded by PLIP K.17: 19 residues within 4Å: Chain C: G.77, Y.78 Chain F: G.77, Y.78 Chain I: G.77, Y.78 Chain L: G.77, Y.78 Ligands: K.5, K.6, K.8, K.14, K.15, K.23, K.24, K.26, K.32, K.33, K.35 Ligand excluded by PLIP K.21: 19 residues within 4Å: Chain C: T.75, V.76 Chain F: T.75, V.76 Chain I: T.75, V.76 Chain L: T.75, V.76 Ligands: K.3, K.4, K.5, K.12, K.13, K.14, K.22, K.23, K.30, K.31, K.32 Ligand excluded by PLIP K.22: 15 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: TBA.2, K.3, K.4, TBA.11, K.12, K.13, TBA.20, K.21, TBA.29, K.30, K.31 Ligand excluded by PLIP K.23: 19 residues within 4Å: Chain C: V.76, G.77 Chain F: V.76, G.77 Chain I: V.76, G.77 Chain L: V.76, G.77 Ligands: K.3, K.5, K.8, K.12, K.14, K.17, K.21, K.26, K.30, K.32, K.35 Ligand excluded by PLIP K.24: 15 residues within 4Å: Chain C: Y.78 Chain F: Y.78 Chain I: Y.78 Chain L: Y.78 Ligands: K.6, K.7, K.8, K.15, K.16, K.17, K.25, K.26, K.33, K.34, K.35 Ligand excluded by PLIP K.25: 7 residues within 4Å: Ligands: K.6, K.7, K.15, K.16, K.24, K.33, K.34 Ligand excluded by PLIP K.26: 19 residues within 4Å: Chain C: G.77, Y.78 Chain F: G.77, Y.78 Chain I: G.77, Y.78 Chain L: G.77, Y.78 Ligands: K.5, K.6, K.8, K.14, K.15, K.17, K.23, K.24, K.32, K.33, K.35 Ligand excluded by PLIP K.30: 19 residues within 4Å: Chain C: T.75, V.76 Chain F: T.75, V.76 Chain I: T.75, V.76 Chain L: T.75, V.76 Ligands: K.3, K.4, K.5, K.12, K.13, K.14, K.21, K.22, K.23, K.31, K.32 Ligand excluded by PLIP K.31: 15 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: TBA.2, K.3, K.4, TBA.11, K.12, K.13, TBA.20, K.21, K.22, TBA.29, K.30 Ligand excluded by PLIP K.32: 19 residues within 4Å: Chain C: V.76, G.77 Chain F: V.76, G.77 Chain I: V.76, G.77 Chain L: V.76, G.77 Ligands: K.3, K.5, K.8, K.12, K.14, K.17, K.21, K.23, K.26, K.30, K.35 Ligand excluded by PLIP K.33: 15 residues within 4Å: Chain C: Y.78 Chain F: Y.78 Chain I: Y.78 Chain L: Y.78 Ligands: K.6, K.7, K.8, K.15, K.16, K.17, K.24, K.25, K.26, K.34, K.35 Ligand excluded by PLIP K.34: 7 residues within 4Å: Ligands: K.6, K.7, K.15, K.16, K.24, K.25, K.33 Ligand excluded by PLIP K.35: 19 residues within 4Å: Chain C: G.77, Y.78 Chain F: G.77, Y.78 Chain I: G.77, Y.78 Chain L: G.77, Y.78 Ligands: K.5, K.6, K.8, K.14, K.15, K.17, K.23, K.24, K.26, K.32, K.33 Ligand excluded by PLIP

4 x DGA: DIACYL GLYCEROL(Non-covalent)

DGA.9: 11 residues within 4Å: Chain C: T.85, L.86, R.89, L.90 Chain K: E.53 Chain L: Y.45, Y.62, P.63, R.64, L.66, F.67 11 PLIP interactions: 4 interactions with chain C, 6 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: C:L.86, C:L.86, C:L.90, L:Y.45, L:Y.45, L:Y.62, L:L.66, L:L.66, L:F.67 Hydrogen bonds: C:R.89, K:E.53 DGA.18: 11 residues within 4Å: Chain F: T.85, L.86, R.89, L.90 Chain H: E.53 Chain I: Y.45, Y.62, P.63, R.64, L.66, F.67 11 PLIP interactions: 4 interactions with chain F, 6 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: F:L.86, F:L.86, F:L.90, I:Y.45, I:Y.45, I:Y.62, I:L.66, I:L.66, I:F.67 Hydrogen bonds: F:R.89, H:E.53 DGA.27: 11 residues within 4Å: Chain B: E.53 Chain C: Y.45, Y.62, P.63, R.64, L.66, F.67 Chain I: T.85, L.86, R.89, L.90 11 PLIP interactions: 6 interactions with chain C, 4 interactions with chain I, 1 interactions with chain B Hydrophobic interactions: C:Y.45, C:Y.45, C:Y.62, C:L.66, C:L.66, C:F.67, I:L.86, I:L.86, I:L.90 Hydrogen bonds: I:R.89, B:E.53 DGA.36: 11 residues within 4Å: Chain E: E.53 Chain F: Y.45, Y.62, P.63, R.64, L.66, F.67 Chain L: T.85, L.86, R.89, L.90 11 PLIP interactions: 6 interactions with chain F, 4 interactions with chain L, 1 interactions with chain E Hydrophobic interactions: F:Y.45, F:Y.45, F:Y.62, F:L.66, F:L.66, F:F.67, L:L.86, L:L.86, L:L.90 Hydrogen bonds: L:R.89, E:E.53

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

Fab heavy chain: ADGJ
Fab light chain: BEHK
pH-gated potassium channel KcsA: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

D
D

G
D

J
D

B
E

E
E

H
E

K
E

C
F

F
F

I
F

L
F

Membrane

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

Fab light chain

pH-gated potassium channel KcsA

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