SMTL ID : 3e86.2 (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 CS: CESIUM ION(Non-covalent)

CS.1: 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.5, NA.8, CS.9, NA.12, CS.13, NA.16 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 CS.5: 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.1, NA.4, NA.8, CS.9, NA.12, CS.13, NA.16 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 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.1, NA.4, CS.5, NA.8, NA.12, CS.13, NA.16 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 CS.13: 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.1, NA.4, CS.5, NA.8, CS.9, NA.12, NA.16 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 MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 3 residues within 4Å: Chain A: L.15, I.18, S.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.15, A:I.18 MPD.6: 3 residues within 4Å: Chain B: L.15, I.18, S.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.15, B:I.18 MPD.10: 3 residues within 4Å: Chain C: L.15, I.18, S.19 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.15, C:I.18 MPD.14: 3 residues within 4Å: Chain D: L.15, I.18, S.19 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.15, D:I.18

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

NA.3: 7 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.7, NA.11, NA.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.45 NA.4: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: CS.1, CS.5, NA.8, CS.9, NA.12, CS.13, NA.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.46 NA.7: 7 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.3, NA.11, NA.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.45 NA.8: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: CS.1, NA.4, CS.5, CS.9, NA.12, CS.13, NA.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.46 NA.11: 7 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: NA.3, NA.7, NA.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C: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.1, NA.4, CS.5, NA.8, CS.9, CS.13, NA.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C: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.3, NA.7, NA.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.45 NA.16: 11 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: CS.1, NA.4, CS.5, NA.8, CS.9, NA.12, CS.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.46

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
B

B
B

C
B

D
B

Membrane

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

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