SMTL ID : 6cpv.1 (1 other biounit)

MicroED structure of NaK ion channel reveals a process of Na+ partition into the selectivity filter

Coordinates

PDB Format Compare

Method

ELECTRON CRYSTALLOGRAPHY 2.50 Å

Oligo State

homo-tetramer

Ligands

32 x NA: SODIUM ION(Non-functional Binders)

NA.1: 19 residues within 4Å: Chain A: T.45, V.46 Chain B: T.45, V.46 Chain C: T.45, V.46 Chain D: T.45, V.46 Ligands: NA.3, NA.4, NA.10, NA.12, NA.13, NA.19, NA.21, NA.22, NA.28, NA.30, NA.31 Ligand excluded by PLIP NA.2: 11 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: NA.8, NA.11, NA.17, NA.20, NA.26, NA.29, NA.35 Ligand excluded by PLIP NA.3: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: NA.1, NA.10, NA.12, NA.19, NA.21, NA.28, NA.30 Ligand excluded by PLIP NA.4: 15 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.1, NA.5, NA.10, NA.13, NA.14, NA.19, NA.22, NA.23, NA.28, NA.31, NA.32 Ligand excluded by PLIP NA.5: 11 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.4, NA.13, NA.14, NA.22, NA.23, NA.31, NA.32 Ligand excluded by PLIP NA.6: 3 residues within 4Å: Ligands: NA.15, NA.24, NA.33 Ligand excluded by PLIP NA.7: 3 residues within 4Å: Ligands: NA.16, NA.25, NA.34 Ligand excluded by PLIP NA.8: 7 residues within 4Å: Ligands: NA.2, NA.11, NA.17, NA.20, NA.26, NA.29, NA.35 Ligand excluded by PLIP NA.10: 19 residues within 4Å: Chain A: T.45, V.46 Chain B: T.45, V.46 Chain C: T.45, V.46 Chain D: T.45, V.46 Ligands: NA.1, NA.3, NA.4, NA.12, NA.13, NA.19, NA.21, NA.22, NA.28, NA.30, NA.31 Ligand excluded by PLIP NA.11: 11 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: NA.2, NA.8, NA.17, NA.20, NA.26, NA.29, NA.35 Ligand excluded by PLIP NA.12: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: NA.1, NA.3, NA.10, NA.19, NA.21, NA.28, NA.30 Ligand excluded by PLIP NA.13: 15 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.1, NA.4, NA.5, NA.10, NA.14, NA.19, NA.22, NA.23, NA.28, NA.31, NA.32 Ligand excluded by PLIP NA.14: 11 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.4, NA.5, NA.13, NA.22, NA.23, NA.31, NA.32 Ligand excluded by PLIP NA.15: 3 residues within 4Å: Ligands: NA.6, NA.24, NA.33 Ligand excluded by PLIP NA.16: 3 residues within 4Å: Ligands: NA.7, NA.25, NA.34 Ligand excluded by PLIP NA.17: 7 residues within 4Å: Ligands: NA.2, NA.8, NA.11, NA.20, NA.26, NA.29, NA.35 Ligand excluded by PLIP NA.19: 19 residues within 4Å: Chain A: T.45, V.46 Chain B: T.45, V.46 Chain C: T.45, V.46 Chain D: T.45, V.46 Ligands: NA.1, NA.3, NA.4, NA.10, NA.12, NA.13, NA.21, NA.22, NA.28, NA.30, NA.31 Ligand excluded by PLIP NA.20: 11 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: NA.2, NA.8, NA.11, NA.17, NA.26, NA.29, NA.35 Ligand excluded by PLIP NA.21: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: NA.1, NA.3, NA.10, NA.12, NA.19, NA.28, NA.30 Ligand excluded by PLIP NA.22: 15 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.1, NA.4, NA.5, NA.10, NA.13, NA.14, NA.19, NA.23, NA.28, NA.31, NA.32 Ligand excluded by PLIP NA.23: 11 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.4, NA.5, NA.13, NA.14, NA.22, NA.31, NA.32 Ligand excluded by PLIP NA.24: 3 residues within 4Å: Ligands: NA.6, NA.15, NA.33 Ligand excluded by PLIP NA.25: 3 residues within 4Å: Ligands: NA.7, NA.16, NA.34 Ligand excluded by PLIP NA.26: 7 residues within 4Å: Ligands: NA.2, NA.8, NA.11, NA.17, NA.20, NA.29, NA.35 Ligand excluded by PLIP NA.28: 19 residues within 4Å: Chain A: T.45, V.46 Chain B: T.45, V.46 Chain C: T.45, V.46 Chain D: T.45, V.46 Ligands: NA.1, NA.3, NA.4, NA.10, NA.12, NA.13, NA.19, NA.21, NA.22, NA.30, NA.31 Ligand excluded by PLIP NA.29: 11 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: NA.2, NA.8, NA.11, NA.17, NA.20, NA.26, NA.35 Ligand excluded by PLIP NA.30: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: NA.1, NA.3, NA.10, NA.12, NA.19, NA.21, NA.28 Ligand excluded by PLIP NA.31: 15 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.1, NA.4, NA.5, NA.10, NA.13, NA.14, NA.19, NA.22, NA.23, NA.28, NA.32 Ligand excluded by PLIP NA.32: 11 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.4, NA.5, NA.13, NA.14, NA.22, NA.23, NA.31 Ligand excluded by PLIP NA.33: 3 residues within 4Å: Ligands: NA.6, NA.15, NA.24 Ligand excluded by PLIP NA.34: 3 residues within 4Å: Ligands: NA.7, NA.16, NA.25 Ligand excluded by PLIP NA.35: 7 residues within 4Å: Ligands: NA.2, NA.8, NA.11, NA.17, NA.20, NA.26, NA.29 Ligand excluded by PLIP

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

MPD.9: 4 residues within 4Å: Chain A: L.15, T.16, S.19, Y.65 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.65 Hydrogen bonds: A:S.19, A:S.19 MPD.18: 4 residues within 4Å: Chain B: L.15, T.16, S.19, Y.65 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.65 Hydrogen bonds: B:S.19, B:S.19 MPD.27: 4 residues within 4Å: Chain C: L.15, T.16, S.19, Y.65 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.65 Hydrogen bonds: C:S.19, C:S.19 MPD.36: 4 residues within 4Å: Chain D: L.15, T.16, S.19, Y.65 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.65 Hydrogen bonds: D:S.19, D:S.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., MicroED structure of the NaK ion channel reveals a Na+partition process into the selectivity filter. Commun Biol (2018)

Release Date

2018-09-12

Peptides

Potassium channel protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Membrane

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

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