SMTL ID : 7oph.1

NaK S-DI mutant with Na+ and K+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-tetramer

Ligands

12 x K: POTASSIUM ION(Non-covalent)

K.1: 7 residues within 4Å: Chain A: T.46 Chain B: T.46 Chain C: T.46 Chain D: T.46 Ligands: K.14, K.26, K.39 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 interactions with chain D Metal complexes: B:T.46, B:T.46, A:T.46, D:T.46, D:T.46 K.2: 4 residues within 4Å: Chain A: S.52, P.53, Q.54 Ligands: MPD.48 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.52, A:S.52, H2O.2 K.3: 5 residues within 4Å: Chain A: D.50 Chain B: D.50 Chain C: D.50 Chain D: D.50 Ligands: K.28 No protein-ligand interaction detected (PLIP) K.4: 8 residues within 4Å: Chain A: V.47, G.48, S.49 Chain B: G.48, S.49 Ligands: K.15, K.29, K.40 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:V.47 K.14: 14 residues within 4Å: Chain A: T.46, V.47 Chain B: T.46, V.47, G.48 Chain C: T.46, V.47, G.48 Chain D: T.46, V.47, G.48 Ligands: K.1, K.26, K.39 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Metal complexes: A:V.47, C:T.46, C:V.47, B:V.47, D:T.46 K.15: 8 residues within 4Å: Chain B: V.47, G.48, S.49 Chain C: G.48, S.49 Ligands: K.4, K.29, K.40 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:S.49, C:S.49 K.26: 7 residues within 4Å: Chain A: T.46 Chain B: T.46 Chain C: T.46 Chain D: T.46 Ligands: K.1, K.14, K.39 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 interactions with chain D Metal complexes: C:T.46, B:T.46, B:T.46, D:T.46, D:T.46 K.27: 4 residues within 4Å: Chain C: S.52, P.53, Q.54 Ligands: MPD.23 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.52, C:S.52, H2O.5 K.28: 5 residues within 4Å: Chain A: D.50 Chain B: D.50 Chain C: D.50 Chain D: D.50 Ligands: K.3 No protein-ligand interaction detected (PLIP) K.29: 8 residues within 4Å: Chain C: V.47, G.48, S.49 Chain D: G.48, S.49 Ligands: K.4, K.15, K.40 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:V.47 K.39: 14 residues within 4Å: Chain A: T.46, V.47, G.48 Chain B: T.46, V.47, G.48 Chain C: T.46, V.47 Chain D: T.46, V.47, G.48 Ligands: K.1, K.14, K.26 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D, 2 interactions with chain A Metal complexes: B:T.46, C:V.47, D:V.47, A:T.46, A:V.47 K.40: 8 residues within 4Å: Chain A: G.48, S.49 Chain D: V.47, G.48, S.49 Ligands: K.4, K.15, K.29 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Metal complexes: D:S.49, A:S.49

22 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 11 residues within 4Å: Chain A: L.10, L.13, G.71, L.72, G.75 Chain D: A.81, Q.85, L.86, I.89 Ligands: MPD.47, MRD.50 Ligand excluded by PLIP MPD.6: 4 residues within 4Å: Chain A: P.87, L.90, S.91, V.94 Ligand excluded by PLIP MPD.7: 2 residues within 4Å: Chain A: I.60 Ligands: MPD.46 Ligand excluded by PLIP MPD.16: 13 residues within 4Å: Chain A: F.11, T.14, I.15, L.18, F.76, L.80 Chain B: I.63, L.64, F.67, I.68 Ligands: MRD.11, MRD.13, MPD.17 Ligand excluded by PLIP MPD.17: 4 residues within 4Å: Chain B: L.64, I.68 Ligands: MRD.13, MPD.16 Ligand excluded by PLIP MPD.18: 8 residues within 4Å: Chain A: V.84 Chain B: L.13, L.16, T.17, S.20, I.68, L.72 Ligands: MPD.19 Ligand excluded by PLIP MPD.19: 5 residues within 4Å: Chain A: V.84, S.88 Chain B: L.13, L.16 Ligands: MPD.18 Ligand excluded by PLIP MPD.20: 10 residues within 4Å: Chain B: F.11, T.14, I.15, L.18, F.76, L.80 Chain C: I.63, L.64, F.67 Ligands: MPD.21 Ligand excluded by PLIP MPD.21: 7 residues within 4Å: Chain B: I.34, L.37 Chain C: I.60, I.63, L.64 Ligands: MPD.20, MPD.32 Ligand excluded by PLIP MPD.22: 10 residues within 4Å: Chain B: V.84, Q.85, S.88, I.89, N.92 Chain C: L.13, I.68, L.72 Ligands: MPD.30, MRD.34 Ligand excluded by PLIP MPD.23: 10 residues within 4Å: Chain B: L.31, D.35, Y.38, F.39, S.49, D.50, I.51 Chain C: S.52, K.59 Ligands: K.27 Ligand excluded by PLIP MPD.30: 11 residues within 4Å: Chain B: A.81, Q.85, L.86, I.89 Chain C: L.10, L.13, G.71, L.72, G.75 Ligands: MPD.22, MRD.25 Ligand excluded by PLIP MPD.31: 4 residues within 4Å: Chain C: P.87, L.90, S.91, V.94 Ligand excluded by PLIP MPD.32: 2 residues within 4Å: Chain C: I.60 Ligands: MPD.21 Ligand excluded by PLIP MPD.41: 13 residues within 4Å: Chain C: F.11, T.14, I.15, L.18, F.76, L.80 Chain D: I.63, L.64, F.67, I.68 Ligands: MRD.36, MRD.38, MPD.42 Ligand excluded by PLIP MPD.42: 4 residues within 4Å: Chain D: L.64, I.68 Ligands: MRD.38, MPD.41 Ligand excluded by PLIP MPD.43: 8 residues within 4Å: Chain C: V.84 Chain D: L.13, L.16, T.17, S.20, I.68, L.72 Ligands: MPD.44 Ligand excluded by PLIP MPD.44: 5 residues within 4Å: Chain C: V.84, S.88 Chain D: L.13, L.16 Ligands: MPD.43 Ligand excluded by PLIP MPD.45: 10 residues within 4Å: Chain A: I.63, L.64, F.67 Chain D: F.11, T.14, I.15, L.18, F.76, L.80 Ligands: MPD.46 Ligand excluded by PLIP MPD.46: 7 residues within 4Å: Chain A: I.60, I.63, L.64 Chain D: I.34, L.37 Ligands: MPD.7, MPD.45 Ligand excluded by PLIP MPD.47: 10 residues within 4Å: Chain A: L.13, I.68, L.72 Chain D: V.84, Q.85, S.88, I.89, N.92 Ligands: MPD.5, MRD.9 Ligand excluded by PLIP MPD.48: 10 residues within 4Å: Chain A: S.52, K.59 Chain D: L.31, D.35, Y.38, F.39, S.49, D.50, I.51 Ligands: K.2 Ligand excluded by PLIP

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 1 residues within 4Å: Chain A: S.91 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain B: R.32, P.33, I.34 Ligand excluded by PLIP CL.33: 1 residues within 4Å: Chain C: S.91 Ligand excluded by PLIP CL.49: 3 residues within 4Å: Chain D: R.32, P.33, I.34 Ligand excluded by PLIP

12 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.9: 8 residues within 4Å: Chain A: L.13, L.16, T.17, S.20, Y.65, I.68 Ligands: MRD.10, MPD.47 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.16 MRD.10: 5 residues within 4Å: Chain A: L.16, I.19, S.20, I.23 Ligands: MRD.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.19, A:I.23 Hydrogen bonds: A:L.16 MRD.11: 8 residues within 4Å: Chain A: I.15, L.18, I.19, L.37, V.41 Chain B: I.63, F.67 Ligands: MPD.16 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.63, A:I.15, A:L.18, A:L.18, A:L.37 MRD.12: 3 residues within 4Å: Chain A: E.6 Chain D: L.86, L.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.6, A:E.6 MRD.13: 7 residues within 4Å: Chain A: F.7, L.80, N.83, V.84 Chain B: I.68 Ligands: MPD.16, MPD.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.7, A:L.80 MRD.25: 8 residues within 4Å: Chain B: F.74, I.77, H.78, A.81 Chain C: I.70, G.71, F.74 Ligands: MPD.30 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.74, B:I.77 Hydrogen bonds: B:H.78 MRD.34: 8 residues within 4Å: Chain C: L.13, L.16, T.17, S.20, Y.65, I.68 Ligands: MPD.22, MRD.35 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.16 MRD.35: 5 residues within 4Å: Chain C: L.16, I.19, S.20, I.23 Ligands: MRD.34 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.19, C:I.23 Hydrogen bonds: C:L.16 MRD.36: 8 residues within 4Å: Chain C: I.15, L.18, I.19, L.37, V.41 Chain D: I.63, F.67 Ligands: MPD.41 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.15, C:L.18, C:L.18, C:L.37, D:I.63 MRD.37: 3 residues within 4Å: Chain B: L.86, L.90 Chain C: E.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.6 MRD.38: 7 residues within 4Å: Chain C: F.7, L.80, N.83, V.84 Chain D: I.68 Ligands: MPD.41, MPD.42 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.7, C:L.80 MRD.50: 8 residues within 4Å: Chain A: I.70, G.71, F.74 Chain D: F.74, I.77, H.78, A.81 Ligands: MPD.5 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.74, D:I.77 Hydrogen bonds: D:H.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minniberger, S. et al., Asymmetry and Ion Selectivity Properties of Bacterial Channel NaK Mutants Derived from Ionotropic Glutamate Receptors. J.Mol.Biol. (2023)

Release Date

2022-06-08

Peptides

Potassium channel protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Membrane

We predict this structure to be a membrane protein.
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Potassium channel protein

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