SMTL ID : 3e86.1 (1 other biounit)

High resolution Crystal Structure of the open NaK channel pore

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

MPD.1: 5 residues within 4Å: Chain A: D.34, Y.37, D.48, N.50, F.51 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.37 Hydrogen bonds: A:D.48 MPD.6: 5 residues within 4Å: Chain B: D.34, Y.37, D.48, N.50, F.51 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.37 Hydrogen bonds: B:D.48 MPD.11: 5 residues within 4Å: Chain C: D.34, Y.37, D.48, N.50, F.51 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.37 Hydrogen bonds: C:D.48 MPD.16: 5 residues within 4Å: Chain D: D.34, Y.37, D.48, N.50, F.51 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.37 Hydrogen bonds: D:D.48

4 x CS: CESIUM ION(Non-covalent)

CS.2: 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.4, CS.7, NA.9, CS.12, NA.14, CS.17, NA.19 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Metal complexes: C:T.45, A:T.45, D:T.45, B:T.45 CS.7: 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.2, NA.4, NA.9, CS.12, NA.14, CS.17, NA.19 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Metal complexes: C:T.45, A:T.45, D:T.45, B:T.45 CS.12: 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.2, NA.4, CS.7, NA.9, NA.14, CS.17, NA.19 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Metal complexes: C:T.45, A:T.45, D:T.45, B:T.45 CS.17: 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.2, NA.4, CS.7, NA.9, CS.12, NA.14, NA.19 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Metal complexes: A:T.45, C:T.45, D:T.45, B:T.45

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: CA.8, CA.13, CA.18 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: D:G.49, B:G.49, C:G.49, A:G.49 CA.8: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: CA.3, CA.13, CA.18 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: D:G.49, B:G.49, C:G.49, A:G.49 CA.13: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: CA.3, CA.8, CA.18 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: D:G.49, B:G.49, C:G.49, A:G.49 CA.18: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: CA.3, CA.8, CA.13 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

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

NA.4: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: CS.2, CS.7, NA.9, CS.12, NA.14, CS.17, NA.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.46 NA.5: 7 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.10, NA.15, NA.20 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:T.45, A:T.45, A:T.45, D:T.45, B:T.45 NA.9: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: CS.2, NA.4, CS.7, CS.12, NA.14, CS.17, NA.19 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.46 NA.10: 7 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.5, NA.15, NA.20 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:T.45, A:T.45, A:T.45, D:T.45, B:T.45 NA.14: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: CS.2, NA.4, CS.7, NA.9, CS.12, CS.17, NA.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.46 NA.15: 7 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.5, NA.10, NA.20 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:T.45, A:T.45, A:T.45, D:T.45, B:T.45 NA.19: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: CS.2, NA.4, CS.7, NA.9, CS.12, NA.14, CS.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.46 NA.20: 7 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.5, NA.10, NA.15 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: A:T.45, A:T.45, C:T.45, D:T.45, B:T.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alam, A. et al., High-resolution structure of the open 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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