SMTL ID : 3k08.2 (1 other biounit)

Crystal Structure of CNG mimicking NaK mutant, NaK-NTPP, Na+ complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-tetramer

Ligands

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

MPD.1: 5 residues within 4Å: Chain A: F.11, I.15, L.80 Chain D: L.64, F.67 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.15, A:L.80, D:L.64, D:F.67 MPD.2: 8 residues within 4Å: Chain A: L.10, G.71, L.72, G.75 Chain C: A.81, Q.85, L.86, I.89 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Q.85, C:L.86, C:I.89 MPD.7: 5 residues within 4Å: Chain B: F.11, I.15, L.80 Chain C: L.64, F.67 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.15, B:L.80, C:L.64, C:F.67 MPD.8: 8 residues within 4Å: Chain B: L.10, G.71, L.72, G.75 Chain D: A.81, Q.85, L.86, I.89 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Q.85, D:L.86, D:I.89 MPD.13: 5 residues within 4Å: Chain A: L.64, F.67 Chain C: F.11, I.15, L.80 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.64, A:F.67, C:I.15, C:L.80 MPD.14: 8 residues within 4Å: Chain B: A.81, Q.85, L.86, I.89 Chain C: L.10, G.71, L.72, G.75 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.85, B:L.86, B:I.89 MPD.19: 5 residues within 4Å: Chain B: L.64, F.67 Chain D: F.11, I.15, L.80 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:L.64, B:F.67, D:I.15, D:L.80 MPD.20: 8 residues within 4Å: Chain A: A.81, Q.85, L.86, I.89 Chain D: L.10, G.71, L.72, G.75 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.85, A:L.86, A:I.89

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

NA.3: 15 residues within 4Å: Chain A: T.46, V.47 Chain B: T.46, V.47 Chain C: T.46, V.47 Chain D: T.46, V.47 Ligands: NA.6, NA.9, NA.12, NA.15, NA.18, NA.21, NA.24 Ligand excluded by PLIP NA.4: 7 residues within 4Å: Chain A: T.46 Chain B: T.46 Chain C: T.46 Chain D: T.46 Ligands: NA.10, NA.16, NA.22 Ligand excluded by PLIP NA.5: 11 residues within 4Å: Chain A: G.48 Chain B: G.48 Chain C: G.48 Chain D: G.48 Ligands: NA.6, NA.11, NA.12, NA.17, NA.18, NA.23, NA.24 Ligand excluded by PLIP NA.6: 19 residues within 4Å: Chain A: T.46, V.47 Chain B: T.46, V.47 Chain C: T.46, V.47 Chain D: T.46, V.47 Ligands: NA.3, NA.5, NA.9, NA.11, NA.12, NA.15, NA.17, NA.18, NA.21, NA.23, NA.24 Ligand excluded by PLIP NA.9: 15 residues within 4Å: Chain A: T.46, V.47 Chain B: T.46, V.47 Chain C: T.46, V.47 Chain D: T.46, V.47 Ligands: NA.3, NA.6, NA.12, NA.15, NA.18, NA.21, NA.24 Ligand excluded by PLIP NA.10: 7 residues within 4Å: Chain A: T.46 Chain B: T.46 Chain C: T.46 Chain D: T.46 Ligands: NA.4, NA.16, NA.22 Ligand excluded by PLIP NA.11: 11 residues within 4Å: Chain A: G.48 Chain B: G.48 Chain C: G.48 Chain D: G.48 Ligands: NA.5, NA.6, NA.12, NA.17, NA.18, NA.23, NA.24 Ligand excluded by PLIP NA.12: 19 residues within 4Å: Chain A: T.46, V.47 Chain B: T.46, V.47 Chain C: T.46, V.47 Chain D: T.46, V.47 Ligands: NA.3, NA.5, NA.6, NA.9, NA.11, NA.15, NA.17, NA.18, NA.21, NA.23, NA.24 Ligand excluded by PLIP NA.15: 15 residues within 4Å: Chain A: T.46, V.47 Chain B: T.46, V.47 Chain C: T.46, V.47 Chain D: T.46, V.47 Ligands: NA.3, NA.6, NA.9, NA.12, NA.18, NA.21, NA.24 Ligand excluded by PLIP NA.16: 7 residues within 4Å: Chain A: T.46 Chain B: T.46 Chain C: T.46 Chain D: T.46 Ligands: NA.4, NA.10, NA.22 Ligand excluded by PLIP NA.17: 11 residues within 4Å: Chain A: G.48 Chain B: G.48 Chain C: G.48 Chain D: G.48 Ligands: NA.5, NA.6, NA.11, NA.12, NA.18, NA.23, NA.24 Ligand excluded by PLIP NA.18: 19 residues within 4Å: Chain A: T.46, V.47 Chain B: T.46, V.47 Chain C: T.46, V.47 Chain D: T.46, V.47 Ligands: NA.3, NA.5, NA.6, NA.9, NA.11, NA.12, NA.15, NA.17, NA.21, NA.23, NA.24 Ligand excluded by PLIP NA.21: 15 residues within 4Å: Chain A: T.46, V.47 Chain B: T.46, V.47 Chain C: T.46, V.47 Chain D: T.46, V.47 Ligands: NA.3, NA.6, NA.9, NA.12, NA.15, NA.18, NA.24 Ligand excluded by PLIP NA.22: 7 residues within 4Å: Chain A: T.46 Chain B: T.46 Chain C: T.46 Chain D: T.46 Ligands: NA.4, NA.10, NA.16 Ligand excluded by PLIP NA.23: 11 residues within 4Å: Chain A: G.48 Chain B: G.48 Chain C: G.48 Chain D: G.48 Ligands: NA.5, NA.6, NA.11, NA.12, NA.17, NA.18, NA.24 Ligand excluded by PLIP NA.24: 19 residues within 4Å: Chain A: T.46, V.47 Chain B: T.46, V.47 Chain C: T.46, V.47 Chain D: T.46, V.47 Ligands: NA.3, NA.5, NA.6, NA.9, NA.11, NA.12, NA.15, NA.17, NA.18, NA.21, NA.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Derebe, M.G. et al., Structural studies of ion permeation and Ca2+ blockage of a bacterial channel mimicking the cyclic nucleotide-gated channel pore. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-01-12

Peptides

Potassium channel protein NaK: 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 NaK

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