SMTL ID : 3e8f.1 (1 other biounit)

Crystal Structure of the the open NaK channel- K+/Ba2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 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.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.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.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

8 x BA: BARIUM ION(Non-covalent)

BA.2: 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: K.4, K.5, BA.8, K.10, K.11, BA.14, K.16, K.17, BA.20, K.22, K.23 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:T.45, B:V.46, D:V.46, A:V.46, C:V.46 BA.3: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: BA.9, BA.15, BA.21 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.49, H2O.1, H2O.2, H2O.3, H2O.4 BA.8: 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: BA.2, K.4, K.5, K.10, K.11, BA.14, K.16, K.17, BA.20, K.22, K.23 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:T.45, B:V.46, D:V.46, A:V.46, C:V.46 BA.9: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: BA.3, BA.15, BA.21 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.49, H2O.1, H2O.2, H2O.3, H2O.4 BA.14: 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: BA.2, K.4, K.5, BA.8, K.10, K.11, K.16, K.17, BA.20, K.22, K.23 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:T.45, B:V.46, D:V.46, A:V.46, C:V.46 BA.15: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: BA.3, BA.9, BA.21 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.49, H2O.1, H2O.2, H2O.3, H2O.4 BA.20: 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: BA.2, K.4, K.5, BA.8, K.10, K.11, BA.14, K.16, K.17, K.22, K.23 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Metal complexes: B:T.45, B:V.46, C:V.46, A:V.46, D:V.46 BA.21: 7 residues within 4Å: Chain A: G.49 Chain B: G.49 Chain C: G.49 Chain D: G.49 Ligands: BA.3, BA.9, BA.15 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.49, H2O.1, H2O.2, H2O.3, H2O.4

12 x K: POTASSIUM ION(Non-covalent)

K.4: 15 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: BA.2, K.6, BA.8, K.10, K.12, BA.14, K.16, K.18, BA.20, K.22, K.24 No protein-ligand interaction detected (PLIP) K.5: 11 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: BA.2, BA.8, K.11, BA.14, K.17, BA.20, K.23 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:T.45, D:T.45, B:T.45, C:T.45 K.6: 11 residues within 4Å: Chain A: D.48 Chain B: D.48 Chain C: D.48 Chain D: D.48 Ligands: K.4, K.10, K.12, K.16, K.18, K.22, K.24 No protein-ligand interaction detected (PLIP) K.10: 15 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: BA.2, K.4, K.6, BA.8, K.12, BA.14, K.16, K.18, BA.20, K.22, K.24 No protein-ligand interaction detected (PLIP) K.11: 11 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: BA.2, K.5, BA.8, BA.14, K.17, BA.20, K.23 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:T.45, D:T.45, B:T.45, C:T.45 K.12: 11 residues within 4Å: Chain A: D.48 Chain B: D.48 Chain C: D.48 Chain D: D.48 Ligands: K.4, K.6, K.10, K.16, K.18, K.22, K.24 No protein-ligand interaction detected (PLIP) K.16: 15 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: BA.2, K.4, K.6, BA.8, K.10, K.12, BA.14, K.18, BA.20, K.22, K.24 No protein-ligand interaction detected (PLIP) K.17: 11 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: BA.2, K.5, BA.8, K.11, BA.14, BA.20, K.23 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: D:T.45, B:T.45, A:T.45, C:T.45 K.18: 11 residues within 4Å: Chain A: D.48 Chain B: D.48 Chain C: D.48 Chain D: D.48 Ligands: K.4, K.6, K.10, K.12, K.16, K.22, K.24 No protein-ligand interaction detected (PLIP) K.22: 15 residues within 4Å: Chain A: V.46 Chain B: V.46 Chain C: V.46 Chain D: V.46 Ligands: BA.2, K.4, K.6, BA.8, K.10, K.12, BA.14, K.16, K.18, BA.20, K.24 No protein-ligand interaction detected (PLIP) K.23: 11 residues within 4Å: Chain A: T.45 Chain B: T.45 Chain C: T.45 Chain D: T.45 Ligands: BA.2, K.5, BA.8, K.11, BA.14, K.17, BA.20 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: D:T.45, B:T.45, A:T.45, C:T.45 K.24: 11 residues within 4Å: Chain A: D.48 Chain B: D.48 Chain C: D.48 Chain D: D.48 Ligands: K.4, K.6, K.10, K.12, K.16, K.18, K.22 No protein-ligand interaction detected (PLIP)

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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