SMTL ID : 4r7c.1 (1 other biounit)

Crystal Structure of CNG mimicking NaK-ETPP mutant cocrystallized with DiMethylammonium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

GLY.1: 4 residues within 4Å: Chain A: F.11, I.15, F.76 Chain D: F.67 No protein-ligand interaction detected (PLIP) GLY.2: 1 residues within 4Å: Chain A: H.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.78 GLY.3: 5 residues within 4Å: Chain A: F.61, L.64, Y.65, I.68 Ligands: MPD.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.61 GLY.4: 2 residues within 4Å: Chain A: K.3, D.4 No protein-ligand interaction detected (PLIP) GLY.5: 1 residues within 4Å: Chain A: S.88 No protein-ligand interaction detected (PLIP) GLY.6: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.6, G.6 GLY.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GLY.14: 3 residues within 4Å: Chain B: T.55, D.56, F.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.56, B:F.57 GLY.15: 4 residues within 4Å: Chain A: L.10, G.71, G.75 Chain B: I.89 No protein-ligand interaction detected (PLIP) GLY.16: 4 residues within 4Å: Chain A: F.67 Chain B: I.15, F.76 Ligands: GLY.18 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.16, G.18 GLY.17: 1 residues within 4Å: Chain B: N.92 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.92 GLY.18: 3 residues within 4Å: Chain B: F.11 Ligands: GLY.16, GLY.21 1 PLIP interactions: 1 Ligand-Ligand interactions Hydrogen bonds: G.16 GLY.19: 1 residues within 4Å: Chain B: T.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.55 GLY.20: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.20, G.20 GLY.21: 2 residues within 4Å: Chain B: I.15 Ligands: GLY.18 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.21, G.21 GLY.22: 2 residues within 4Å: Chain A: F.74 Chain B: H.78 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.78 GLY.40: 4 residues within 4Å: Chain B: F.67 Chain C: F.11, I.15, F.76 No protein-ligand interaction detected (PLIP) GLY.41: 1 residues within 4Å: Chain C: H.78 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.78 GLY.42: 5 residues within 4Å: Chain C: F.61, L.64, Y.65, I.68 Ligands: MPD.49 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.61 GLY.43: 2 residues within 4Å: Chain C: K.3, D.4 No protein-ligand interaction detected (PLIP) GLY.44: 1 residues within 4Å: Chain C: S.88 No protein-ligand interaction detected (PLIP) GLY.45: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.45, G.45 GLY.46: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GLY.53: 3 residues within 4Å: Chain D: T.55, D.56, F.57 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.56, D:F.57 GLY.54: 4 residues within 4Å: Chain C: L.10, G.71, G.75 Chain D: I.89 No protein-ligand interaction detected (PLIP) GLY.55: 4 residues within 4Å: Chain C: F.67 Chain D: I.15, F.76 Ligands: GLY.57 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.55, G.57 GLY.56: 1 residues within 4Å: Chain D: N.92 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.92 GLY.57: 3 residues within 4Å: Chain D: F.11 Ligands: GLY.55, GLY.60 1 PLIP interactions: 1 Ligand-Ligand interactions Hydrogen bonds: G.55 GLY.58: 1 residues within 4Å: Chain D: T.55 No protein-ligand interaction detected (PLIP) GLY.59: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.59, G.59 GLY.60: 2 residues within 4Å: Chain D: I.15 Ligands: GLY.57 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.60, G.60 GLY.61: 2 residues within 4Å: Chain C: F.74 Chain D: H.78 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.78

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

MPD.8: 2 residues within 4Å: Chain A: P.33, I.34 No protein-ligand interaction detected (PLIP) MPD.9: 3 residues within 4Å: Chain A: K.3, Q.8, F.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.11 Hydrogen bonds: A:K.3, A:K.3 MPD.10: 4 residues within 4Å: Chain A: F.57, F.61, L.64 Ligands: GLY.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.64 Hydrogen bonds: G.3 MPD.23: 4 residues within 4Å: Chain B: L.16, I.19, S.20 Ligands: MPD.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.16 Hydrogen bonds: B:L.16 MPD.24: 4 residues within 4Å: Chain B: F.61, L.64, I.68 Ligands: DMN.28 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.61, B:L.64 MPD.25: 3 residues within 4Å: Chain B: S.20, I.23 Ligands: MPD.23 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.23 MPD.26: 5 residues within 4Å: Chain B: E.6, V.9 Chain C: I.89, L.90, L.93 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:E.6, B:E.6, B:V.9, C:L.93 MPD.47: 2 residues within 4Å: Chain C: P.33, I.34 No protein-ligand interaction detected (PLIP) MPD.48: 3 residues within 4Å: Chain C: K.3, Q.8, F.11 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.11 Hydrogen bonds: C:K.3, C:K.3 MPD.49: 4 residues within 4Å: Chain C: F.57, F.61, L.64 Ligands: GLY.42 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.64 MPD.62: 4 residues within 4Å: Chain D: L.16, I.19, S.20 Ligands: MPD.64 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.16 Hydrogen bonds: D:L.16 MPD.63: 4 residues within 4Å: Chain D: F.61, L.64, I.68 Ligands: DMN.67 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.61, D:L.64 MPD.64: 3 residues within 4Å: Chain D: S.20, I.23 Ligands: MPD.62 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.23 MPD.65: 5 residues within 4Å: Chain A: I.89, L.90, L.93 Chain D: E.6, V.9 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:E.6, D:E.6, D:V.9, A:L.93

32 x DMN: DIMETHYLAMINE(Non-covalent)(Non-functional Binders)

DMN.11: 1 residues within 4Å: Chain A: S.20 Ligand excluded by PLIP DMN.12: 1 residues within 4Å: Chain A: A.81 Ligand excluded by PLIP DMN.13: 13 residues within 4Å: Chain A: T.46, V.47, G.48 Chain B: T.46, V.47, G.48 Chain C: T.46, V.47, G.48 Chain D: T.46, V.47, G.48 Ligands: DMN.52 Ligand excluded by PLIP DMN.27: 4 residues within 4Å: Chain B: D.4, K.5, E.6, K.79 Ligand excluded by PLIP DMN.28: 2 residues within 4Å: Chain B: S.20 Ligands: MPD.24 Ligand excluded by PLIP DMN.29: 2 residues within 4Å: Chain B: I.68 Chain C: Q.85 Ligand excluded by PLIP DMN.30: 4 residues within 4Å: Chain B: D.35, F.39, T.50, P.51 Ligand excluded by PLIP DMN.31: 1 residues within 4Å: Chain B: R.32 Ligand excluded by PLIP DMN.32: 1 residues within 4Å: Ligands: DMN.33 Ligand excluded by PLIP DMN.33: 3 residues within 4Å: Chain B: T.27 Ligands: DMN.32, DMN.35 Ligand excluded by PLIP DMN.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMN.35: 1 residues within 4Å: Ligands: DMN.33 Ligand excluded by PLIP DMN.36: 3 residues within 4Å: Chain B: P.52, P.53, Q.54 Ligand excluded by PLIP DMN.37: 1 residues within 4Å: Chain B: I.60 Ligand excluded by PLIP DMN.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMN.39: 1 residues within 4Å: Chain B: Q.85 Ligand excluded by PLIP DMN.50: 1 residues within 4Å: Chain C: S.20 Ligand excluded by PLIP DMN.51: 1 residues within 4Å: Chain C: A.81 Ligand excluded by PLIP DMN.52: 13 residues within 4Å: Chain A: T.46, V.47, G.48 Chain B: T.46, V.47, G.48 Chain C: T.46, V.47, G.48 Chain D: T.46, V.47, G.48 Ligands: DMN.13 Ligand excluded by PLIP DMN.66: 4 residues within 4Å: Chain D: D.4, K.5, E.6, K.79 Ligand excluded by PLIP DMN.67: 2 residues within 4Å: Chain D: S.20 Ligands: MPD.63 Ligand excluded by PLIP DMN.68: 2 residues within 4Å: Chain A: Q.85 Chain D: I.68 Ligand excluded by PLIP DMN.69: 4 residues within 4Å: Chain D: D.35, F.39, T.50, P.51 Ligand excluded by PLIP DMN.70: 1 residues within 4Å: Chain D: R.32 Ligand excluded by PLIP DMN.71: 1 residues within 4Å: Ligands: DMN.72 Ligand excluded by PLIP DMN.72: 3 residues within 4Å: Chain D: T.27 Ligands: DMN.71, DMN.74 Ligand excluded by PLIP DMN.73: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMN.74: 1 residues within 4Å: Ligands: DMN.72 Ligand excluded by PLIP DMN.75: 3 residues within 4Å: Chain D: P.52, P.53, Q.54 Ligand excluded by PLIP DMN.76: 1 residues within 4Å: Chain D: I.60 Ligand excluded by PLIP DMN.77: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMN.78: 1 residues within 4Å: Chain D: Q.85 Ligand excluded by 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
A

B
B

C
A

D
B

Membrane

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

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