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

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

Coordinates

PDB Format

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: 2 residues within 4Å: Chain A: R.57 Chain C: A.50 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.50 F09.10: 2 residues within 4Å: Chain D: R.57 Chain F: A.50 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:A.50 F09.19: 2 residues within 4Å: Chain G: R.57 Chain I: A.50 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:A.50 F09.28: 2 residues within 4Å: Chain J: R.57 Chain L: A.50 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:A.50

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

K.2: 15 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.5, TBA.9, K.11, K.14, TBA.18, K.20, K.23, TBA.27, K.29, K.32, TBA.36 Ligand excluded by PLIP K.3: 7 residues within 4Å: Ligands: K.4, K.12, K.13, K.21, K.22, K.30, K.31 Ligand excluded by PLIP K.4: 7 residues within 4Å: Ligands: K.3, K.12, K.13, K.21, K.22, K.30, K.31 Ligand excluded by PLIP K.5: 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.2, K.6, K.11, K.14, K.15, K.20, K.23, K.24, K.29, K.32, K.33 Ligand excluded by PLIP K.6: 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.5, K.7, K.14, K.15, K.16, K.23, K.24, K.25, K.32, K.33, K.34 Ligand excluded by PLIP K.7: 15 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.6, K.15, K.16, K.24, K.25, K.33, K.34 Ligand excluded by PLIP K.11: 15 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.2, K.5, TBA.9, K.14, TBA.18, K.20, K.23, TBA.27, K.29, K.32, TBA.36 Ligand excluded by PLIP K.12: 7 residues within 4Å: Ligands: K.3, K.4, K.13, K.21, K.22, K.30, K.31 Ligand excluded by PLIP K.13: 7 residues within 4Å: Ligands: K.3, K.4, K.12, K.21, K.22, K.30, K.31 Ligand excluded by PLIP K.14: 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.2, K.5, K.6, K.11, K.15, K.20, K.23, K.24, K.29, K.32, K.33 Ligand excluded by PLIP K.15: 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.5, K.6, K.7, K.14, K.16, K.23, K.24, K.25, K.32, K.33, K.34 Ligand excluded by PLIP K.16: 15 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.6, K.7, K.15, K.24, K.25, K.33, K.34 Ligand excluded by PLIP K.20: 15 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.2, K.5, TBA.9, K.11, K.14, TBA.18, K.23, TBA.27, K.29, K.32, TBA.36 Ligand excluded by PLIP K.21: 7 residues within 4Å: Ligands: K.3, K.4, K.12, K.13, K.22, K.30, K.31 Ligand excluded by PLIP K.22: 7 residues within 4Å: Ligands: K.3, K.4, K.12, K.13, K.21, K.30, K.31 Ligand excluded by PLIP K.23: 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.2, K.5, K.6, K.11, K.14, K.15, K.20, K.24, K.29, K.32, K.33 Ligand excluded by PLIP K.24: 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.5, K.6, K.7, K.14, K.15, K.16, K.23, K.25, K.32, K.33, K.34 Ligand excluded by PLIP K.25: 15 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.6, K.7, K.15, K.16, K.24, K.33, K.34 Ligand excluded by PLIP K.29: 15 residues within 4Å: Chain C: T.75 Chain F: T.75 Chain I: T.75 Chain L: T.75 Ligands: K.2, K.5, TBA.9, K.11, K.14, TBA.18, K.20, K.23, TBA.27, K.32, TBA.36 Ligand excluded by PLIP K.30: 7 residues within 4Å: Ligands: K.3, K.4, K.12, K.13, K.21, K.22, K.31 Ligand excluded by PLIP K.31: 7 residues within 4Å: Ligands: K.3, K.4, K.12, K.13, K.21, K.22, K.30 Ligand excluded by PLIP K.32: 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.2, K.5, K.6, K.11, K.14, K.15, K.20, K.23, K.24, K.29, K.33 Ligand excluded by PLIP K.33: 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.5, K.6, K.7, K.14, K.15, K.16, K.23, K.24, K.25, K.32, K.34 Ligand excluded by PLIP K.34: 15 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.6, K.7, K.15, K.16, K.24, K.25, K.33 Ligand excluded by PLIP

4 x DGA: DIACYL GLYCEROL(Non-covalent)

DGA.8: 13 residues within 4Å: Chain C: T.85, L.86, R.89, L.90, V.93 Chain J: S.31 Chain K: E.53 Chain L: Y.45, Y.62, P.63, R.64, L.66, F.67 9 PLIP interactions: 4 interactions with chain C, 4 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: C:L.86, C:L.90, C:V.93, L:Y.45, L:P.63, L:P.63, L:F.67 Salt bridges: C:R.89 Hydrogen bonds: K:E.53 DGA.17: 13 residues within 4Å: Chain F: T.85, L.86, R.89, L.90, V.93 Chain G: S.31 Chain H: E.53 Chain I: Y.45, Y.62, P.63, R.64, L.66, F.67 9 PLIP interactions: 4 interactions with chain F, 4 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: F:L.86, F:L.90, F:V.93, I:Y.45, I:P.63, I:P.63, I:F.67 Salt bridges: F:R.89 Hydrogen bonds: H:E.53 DGA.26: 13 residues within 4Å: Chain A: S.31 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, V.93 9 PLIP interactions: 4 interactions with chain C, 4 interactions with chain I, 1 interactions with chain B Hydrophobic interactions: C:Y.45, C:P.63, C:P.63, C:F.67, I:L.86, I:L.90, I:V.93 Salt bridges: I:R.89 Hydrogen bonds: B:E.53 DGA.35: 13 residues within 4Å: Chain D: S.31 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, V.93 9 PLIP interactions: 4 interactions with chain F, 4 interactions with chain L, 1 interactions with chain E Hydrophobic interactions: F:Y.45, F:P.63, F:P.63, F:F.67, L:L.86, L:L.90, L:V.93 Salt bridges: L:R.89 Hydrogen bonds: E:E.53

4 x TBA: TETRABUTYLAMMONIUM ION(Non-covalent)

TBA.9: 23 residues within 4Å: Chain C: T.74, T.75, F.103 Chain F: T.74, T.75, F.103 Chain I: A.73, T.75, G.99, I.100, F.103 Chain L: A.73, T.75, G.99, I.100, F.103 Ligands: K.2, K.11, TBA.18, K.20, TBA.27, K.29, TBA.36 10 PLIP interactions: 4 interactions with chain L, 1 interactions with chain F, 4 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: L:T.75, L:I.100, L:I.100, L:F.103, F:F.103, I:T.75, I:I.100, I:I.100, I:F.103, C:F.103 TBA.18: 23 residues within 4Å: Chain C: T.74, T.75, F.103 Chain F: T.74, T.75, F.103 Chain I: A.73, T.75, G.99, I.100, F.103 Chain L: A.73, T.75, G.99, I.100, F.103 Ligands: K.2, TBA.9, K.11, K.20, TBA.27, K.29, TBA.36 10 PLIP interactions: 4 interactions with chain L, 1 interactions with chain F, 4 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: L:T.75, L:I.100, L:I.100, L:F.103, F:F.103, I:T.75, I:I.100, I:I.100, I:F.103, C:F.103 TBA.27: 23 residues within 4Å: Chain C: A.73, T.75, G.99, I.100, 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, F.103 Ligands: K.2, TBA.9, K.11, TBA.18, K.20, K.29, TBA.36 10 PLIP interactions: 4 interactions with chain C, 4 interactions with chain F, 1 interactions with chain L, 1 interactions with chain I Hydrophobic interactions: C:T.75, C:I.100, C:I.100, C:F.103, F:T.75, F:I.100, F:I.100, F:F.103, L:F.103, I:F.103 TBA.36: 23 residues within 4Å: Chain C: A.73, T.75, G.99, I.100, 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, F.103 Ligands: K.2, TBA.9, K.11, TBA.18, K.20, TBA.27, K.29 10 PLIP interactions: 4 interactions with chain C, 4 interactions with chain F, 1 interactions with chain L, 1 interactions with chain I Hydrophobic interactions: C:T.75, C:I.100, C:I.100, C:F.103, F:T.75, F:I.100, F:I.100, F:F.103, L:F.103, I:F.103

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
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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Fab heavy chain

Fab light chain

pH-gated potassium channel KcsA

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