SMTL ID : 7m2i.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 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.21, L.24, W.62, V.66 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.21, C:W.62, C:W.62, C:V.66 F09.9: 5 residues within 4Å: Chain D: R.57 Chain F: L.21, L.24, W.62, V.66 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.21, F:W.62, F:W.62, F:V.66 F09.17: 5 residues within 4Å: Chain G: R.57 Chain I: L.21, L.24, W.62, V.66 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:L.21, I:W.62, I:W.62, I:V.66 F09.25: 5 residues within 4Å: Chain J: R.57 Chain L: L.21, L.24, W.62, V.66 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:L.21, L:W.62, L:W.62, L:V.66

4 x 1EM: (1S)-2-HYDROXY-1-[(NONANOYLOXY)METHYL]ETHYL MYRISTATE(Non-covalent)

1EM.2: 9 residues within 4Å: Chain C: V.59, L.61, R.64 Chain L: S.19, Y.37, P.38, R.39, L.41, V.45 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain L Hydrophobic interactions: C:L.61, L:Y.37, L:P.38, L:V.45 Salt bridges: C:R.64 Hydrogen bonds: L:R.39 1EM.10: 9 residues within 4Å: Chain F: V.59, L.61, R.64 Chain I: S.19, Y.37, P.38, R.39, L.41, V.45 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain F Hydrophobic interactions: I:Y.37, I:P.38, I:V.45, F:L.61 Hydrogen bonds: I:R.39 Salt bridges: F:R.64 1EM.18: 9 residues within 4Å: Chain C: S.19, Y.37, P.38, R.39, L.41, V.45 Chain I: V.59, L.61, R.64 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain I Hydrophobic interactions: C:Y.37, C:P.38, C:V.45, I:L.61 Hydrogen bonds: C:R.39 Salt bridges: I:R.64 1EM.26: 9 residues within 4Å: Chain F: S.19, Y.37, P.38, R.39, L.41, V.45 Chain L: V.59, L.61, R.64 6 PLIP interactions: 2 interactions with chain L, 4 interactions with chain F Hydrophobic interactions: L:L.61, F:Y.37, F:P.38, F:V.45 Salt bridges: L:R.64 Hydrogen bonds: F:R.39

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

K.3: 3 residues within 4Å: Ligands: K.11, K.19, K.27 Ligand excluded by PLIP K.4: 7 residues within 4Å: Chain C: T.50 Chain F: T.50 Chain I: T.50 Chain L: T.50 Ligands: K.12, K.20, K.28 Ligand excluded by PLIP K.5: 11 residues within 4Å: Chain C: G.52, Y.53 Chain F: G.52, Y.53 Chain I: G.52, Y.53 Chain L: G.52, Y.53 Ligands: K.13, K.21, K.29 Ligand excluded by PLIP K.6: 7 residues within 4Å: Ligands: K.7, K.14, K.15, K.22, K.23, K.30, K.31 Ligand excluded by PLIP K.7: 7 residues within 4Å: Ligands: K.6, K.14, K.15, K.22, K.23, K.30, K.31 Ligand excluded by PLIP K.8: 11 residues within 4Å: Chain C: T.50, V.51 Chain F: T.50, V.51 Chain I: T.50, V.51 Chain L: T.50, V.51 Ligands: K.16, K.24, K.32 Ligand excluded by PLIP K.11: 3 residues within 4Å: Ligands: K.3, K.19, K.27 Ligand excluded by PLIP K.12: 7 residues within 4Å: Chain C: T.50 Chain F: T.50 Chain I: T.50 Chain L: T.50 Ligands: K.4, K.20, K.28 Ligand excluded by PLIP K.13: 11 residues within 4Å: Chain C: G.52, Y.53 Chain F: G.52, Y.53 Chain I: G.52, Y.53 Chain L: G.52, Y.53 Ligands: K.5, K.21, K.29 Ligand excluded by PLIP K.14: 7 residues within 4Å: Ligands: K.6, K.7, K.15, K.22, K.23, K.30, K.31 Ligand excluded by PLIP K.15: 7 residues within 4Å: Ligands: K.6, K.7, K.14, K.22, K.23, K.30, K.31 Ligand excluded by PLIP K.16: 11 residues within 4Å: Chain C: T.50, V.51 Chain F: T.50, V.51 Chain I: T.50, V.51 Chain L: T.50, V.51 Ligands: K.8, K.24, K.32 Ligand excluded by PLIP K.19: 3 residues within 4Å: Ligands: K.3, K.11, K.27 Ligand excluded by PLIP K.20: 7 residues within 4Å: Chain C: T.50 Chain F: T.50 Chain I: T.50 Chain L: T.50 Ligands: K.4, K.12, K.28 Ligand excluded by PLIP K.21: 11 residues within 4Å: Chain C: G.52, Y.53 Chain F: G.52, Y.53 Chain I: G.52, Y.53 Chain L: G.52, Y.53 Ligands: K.5, K.13, K.29 Ligand excluded by PLIP K.22: 7 residues within 4Å: Ligands: K.6, K.7, K.14, K.15, K.23, K.30, K.31 Ligand excluded by PLIP K.23: 7 residues within 4Å: Ligands: K.6, K.7, K.14, K.15, K.22, K.30, K.31 Ligand excluded by PLIP K.24: 11 residues within 4Å: Chain C: T.50, V.51 Chain F: T.50, V.51 Chain I: T.50, V.51 Chain L: T.50, V.51 Ligands: K.8, K.16, K.32 Ligand excluded by PLIP K.27: 3 residues within 4Å: Ligands: K.3, K.11, K.19 Ligand excluded by PLIP K.28: 7 residues within 4Å: Chain C: T.50 Chain F: T.50 Chain I: T.50 Chain L: T.50 Ligands: K.4, K.12, K.20 Ligand excluded by PLIP K.29: 11 residues within 4Å: Chain C: G.52, Y.53 Chain F: G.52, Y.53 Chain I: G.52, Y.53 Chain L: G.52, Y.53 Ligands: K.5, K.13, K.21 Ligand excluded by PLIP K.30: 7 residues within 4Å: Ligands: K.6, K.7, K.14, K.15, K.22, K.23, K.31 Ligand excluded by PLIP K.31: 7 residues within 4Å: Ligands: K.6, K.7, K.14, K.15, K.22, K.23, K.30 Ligand excluded by PLIP K.32: 11 residues within 4Å: Chain C: T.50, V.51 Chain F: T.50, V.51 Chain I: T.50, V.51 Chain L: T.50, V.51 Ligands: K.8, K.16, K.24 Ligand excluded by PLIP

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

Monoclonal antibody (IgG) against KcsA, Fab heavy chain: ADGJ
Monoclonal antibody (IgG) against KcsA, 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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Monoclonal antibody (IgG) against KcsA, Fab heavy chain

Monoclonal antibody (IgG) against KcsA, Fab light chain

pH-gated potassium channel KcsA

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