SMTL ID : 3e8g.1 (1 other biounit)

Crystal Structure of the the open NaK channel-Na+/Ca2+ complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

MPD.1: 4 residues within 4Å: Chain A: D.34, Y.37, D.48, F.51 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.37, A:F.51 Hydrogen bonds: A:D.48, A:F.51 MPD.2: 2 residues within 4Å: Chain A: F.61, I.68 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.68 MPD.7: 4 residues within 4Å: Chain B: D.34, Y.37, D.48, F.51 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.37, B:F.51 Hydrogen bonds: B:D.48, B:F.51 MPD.8: 2 residues within 4Å: Chain B: F.61, I.68 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.68 MPD.13: 4 residues within 4Å: Chain C: D.34, Y.37, D.48, F.51 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.37, C:F.51 Hydrogen bonds: C:D.48, C:F.51 MPD.14: 2 residues within 4Å: Chain C: F.61, I.68 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.68 MPD.19: 4 residues within 4Å: Chain D: D.34, Y.37, D.48, F.51 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.37, D:F.51 Hydrogen bonds: D:D.48, D:F.51 MPD.20: 2 residues within 4Å: Chain D: F.61, I.68 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.68

4 x CS: CESIUM ION(Non-covalent)

CS.3: 15 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.6, CS.9, NA.12, CS.15, NA.18, CS.21, NA.24 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: D:T.45, C:T.45, B:T.45, A:T.45 CS.9: 15 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: CS.3, NA.6, NA.12, CS.15, NA.18, CS.21, NA.24 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: D:T.45, C:T.45, B:T.45, A:T.45 CS.15: 15 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: CS.3, NA.6, CS.9, NA.12, NA.18, CS.21, NA.24 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: D:T.45, C:T.45, B:T.45, A:T.45 CS.21: 15 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: CS.3, NA.6, CS.9, NA.12, CS.15, NA.18, NA.24 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A Metal complexes: C:T.45, B:T.45, D:T.45, A:T.45

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: CA.10, CA.16, CA.22 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: D:G.49, A:G.49, B:G.49, C:G.49 CA.10: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: CA.4, CA.16, CA.22 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: D:G.49, A:G.49, B:G.49, C:G.49 CA.16: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: CA.4, CA.10, CA.22 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Metal complexes: B:G.49, C:G.49, A:G.49, D:G.49 CA.22: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: CA.4, CA.10, CA.16 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Metal complexes: B:G.49, C:G.49, A:G.49, D:G.49

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

NA.5: 7 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.11, NA.17, NA.23 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: D:T.45, C:T.45, B:T.45, A:T.45, A:T.45 NA.6: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: CS.3, CS.9, NA.12, CS.15, NA.18, CS.21, NA.24 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:V.46 Water bridges: A:D.48, B:D.48, C:D.48, D:D.48 NA.11: 7 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.5, NA.17, NA.23 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: D:T.45, C:T.45, B:T.45, A:T.45, A:T.45 NA.12: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: CS.3, NA.6, CS.9, CS.15, NA.18, CS.21, NA.24 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:V.46 Water bridges: D:D.48, B:D.48, C:D.48, A:D.48 NA.17: 7 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.5, NA.11, NA.23 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:T.45, B:T.45, A:T.45, A:T.45, D:T.45 NA.18: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: CS.3, NA.6, CS.9, NA.12, CS.15, CS.21, NA.24 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:V.46 Water bridges: B:D.48, C:D.48, A:D.48, D:D.48 NA.23: 7 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.5, NA.11, NA.17 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:T.45, C:T.45, B:T.45, A:T.45, D:T.45 NA.24: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: CS.3, NA.6, CS.9, NA.12, CS.15, NA.18, CS.21 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:V.46 Water bridges: A:D.48, B:D.48, C:D.48, D:D.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alam, A. et al., Structural analysis of ion selectivity in the NaK channel. Nat.Struct.Mol.Biol. (2009)

Release Date

2008-12-23

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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