SMTL ID : 4rai.2 (1 other biounit)

Crystal Structure of CNG mimicking NaK-ETPP mutant in complex with Na+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 15 residues within 4Å: Chain A: V.47, G.48 Chain B: V.47, G.48 Chain C: V.47, G.48 Chain D: V.47, G.48 Ligands: NA.3, NA.14, NA.16, NA.27, NA.29, NA.40, NA.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.47 NA.2: 11 residues within 4Å: Chain A: T.46 Chain B: T.46 Chain C: T.46 Chain D: T.46 Ligands: NA.3, NA.15, NA.16, NA.28, NA.29, NA.41, NA.42 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: B:T.46, C:T.46, D:T.46, D:T.46, A:T.46 NA.3: 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.1, NA.2, NA.14, NA.15, NA.16, NA.27, NA.28, NA.29, NA.40, NA.41, NA.42 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.46 NA.14: 15 residues within 4Å: Chain A: V.47, G.48 Chain B: V.47, G.48 Chain C: V.47, G.48 Chain D: V.47, G.48 Ligands: NA.1, NA.3, NA.16, NA.27, NA.29, NA.40, NA.42 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.47 NA.15: 11 residues within 4Å: Chain A: T.46 Chain B: T.46 Chain C: T.46 Chain D: T.46 Ligands: NA.2, NA.3, NA.16, NA.28, NA.29, NA.41, NA.42 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: B:T.46, C:T.46, D:T.46, D:T.46, A:T.46 NA.16: 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.1, NA.2, NA.3, NA.14, NA.15, NA.27, NA.28, NA.29, NA.40, NA.41, NA.42 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.47 NA.27: 15 residues within 4Å: Chain A: V.47, G.48 Chain B: V.47, G.48 Chain C: V.47, G.48 Chain D: V.47, G.48 Ligands: NA.1, NA.3, NA.14, NA.16, NA.29, NA.40, NA.42 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.47 NA.28: 11 residues within 4Å: Chain A: T.46 Chain B: T.46 Chain C: T.46 Chain D: T.46 Ligands: NA.2, NA.3, NA.15, NA.16, NA.29, NA.41, NA.42 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:T.46, A:T.46, D:T.46, D:T.46, B:T.46 NA.29: 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.1, NA.2, NA.3, NA.14, NA.15, NA.16, NA.27, NA.28, NA.40, NA.41, NA.42 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.47 NA.40: 15 residues within 4Å: Chain A: V.47, G.48 Chain B: V.47, G.48 Chain C: V.47, G.48 Chain D: V.47, G.48 Ligands: NA.1, NA.3, NA.14, NA.16, NA.27, NA.29, NA.42 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.47 NA.41: 11 residues within 4Å: Chain A: T.46 Chain B: T.46 Chain C: T.46 Chain D: T.46 Ligands: NA.2, NA.3, NA.15, NA.16, NA.28, NA.29, NA.42 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:T.46, A:T.46, D:T.46, C:T.46, B:T.46 NA.42: 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.1, NA.2, NA.3, NA.14, NA.15, NA.16, NA.27, NA.28, NA.29, NA.40, NA.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.46

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

MPD.4: 3 residues within 4Å: Chain A: S.20, I.23, F.24 No protein-ligand interaction detected (PLIP) MPD.5: 1 residues within 4Å: Chain A: I.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.19 MPD.6: 1 residues within 4Å: Ligands: GLY.12 No protein-ligand interaction detected (PLIP) MPD.17: 3 residues within 4Å: Chain B: S.20, I.23, F.24 No protein-ligand interaction detected (PLIP) MPD.18: 1 residues within 4Å: Chain B: I.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.19 MPD.19: 1 residues within 4Å: Ligands: GLY.25 No protein-ligand interaction detected (PLIP) MPD.30: 3 residues within 4Å: Chain C: S.20, I.23, F.24 No protein-ligand interaction detected (PLIP) MPD.31: 1 residues within 4Å: Chain C: I.19 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.19 MPD.32: 1 residues within 4Å: Ligands: GLY.38 No protein-ligand interaction detected (PLIP) MPD.43: 3 residues within 4Å: Chain D: S.20, I.23, F.24 No protein-ligand interaction detected (PLIP) MPD.44: 1 residues within 4Å: Chain D: I.19 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.19 MPD.45: 1 residues within 4Å: Ligands: GLY.51 No protein-ligand interaction detected (PLIP)

28 x GLY: GLYCINE(Non-covalent)(Non-functional Binders)

GLY.7: 5 residues within 4Å: Chain A: E.29, F.39, P.51, P.52, P.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.29 GLY.8: 3 residues within 4Å: Chain A: E.6, L.10 Chain D: I.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.6 GLY.9: 3 residues within 4Å: Chain A: F.11 Chain C: L.64, F.67 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.9, G.9 GLY.10: 2 residues within 4Å: Chain A: Q.85, S.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.88, A:S.88 GLY.11: 4 residues within 4Å: Chain A: G.71 Chain D: H.78, A.81, V.82 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.78 GLY.12: 3 residues within 4Å: Chain A: T.22, L.37 Ligands: MPD.6 No protein-ligand interaction detected (PLIP) GLY.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GLY.20: 5 residues within 4Å: Chain B: E.29, F.39, P.51, P.52, P.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.29 GLY.21: 3 residues within 4Å: Chain B: E.6, L.10 Chain C: I.89 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.6 GLY.22: 3 residues within 4Å: Chain B: F.11 Chain D: L.64, F.67 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.22, G.22 GLY.23: 2 residues within 4Å: Chain B: Q.85, S.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.88, B:S.88 GLY.24: 4 residues within 4Å: Chain B: G.71 Chain C: H.78, A.81, V.82 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.78 GLY.25: 3 residues within 4Å: Chain B: T.22, L.37 Ligands: MPD.19 No protein-ligand interaction detected (PLIP) GLY.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GLY.33: 5 residues within 4Å: Chain C: E.29, F.39, P.51, P.52, P.53 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.29 GLY.34: 3 residues within 4Å: Chain A: I.89 Chain C: E.6, L.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.6 GLY.35: 3 residues within 4Å: Chain B: L.64, F.67 Chain C: F.11 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.35, G.35 GLY.36: 2 residues within 4Å: Chain C: Q.85, S.88 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.88, C:S.88 GLY.37: 4 residues within 4Å: Chain A: H.78, A.81, V.82 Chain C: G.71 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.78 GLY.38: 3 residues within 4Å: Chain C: T.22, L.37 Ligands: MPD.32 No protein-ligand interaction detected (PLIP) GLY.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GLY.46: 5 residues within 4Å: Chain D: E.29, F.39, P.51, P.52, P.53 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.29 GLY.47: 3 residues within 4Å: Chain B: I.89 Chain D: E.6, L.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.6 GLY.48: 3 residues within 4Å: Chain A: L.64, F.67 Chain D: F.11 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.48, G.48 GLY.49: 2 residues within 4Å: Chain D: Q.85, S.88 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.88, D:S.88 GLY.50: 4 residues within 4Å: Chain B: H.78, A.81, V.82 Chain D: G.71 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.78 GLY.51: 3 residues within 4Å: Chain D: T.22, L.37 Ligands: MPD.45 No protein-ligand interaction detected (PLIP) GLY.52: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Napolitano, L.M. et al., A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-07-01

Peptides

Potassium channel protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Potassium channel protein

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