SMTL ID : 5wc5.2 (1 other biounit)

Structural insights into the potency of SK/IK channel positive modulators

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: A.53, R.56 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:A.53 Salt bridges: A:R.56 Hydrogen bonds: C:Q.93 SO4.2: 1 residues within 4Å: Chain A: H.52 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.52 SO4.3: 7 residues within 4Å: Chain A: R.35, K.57, H.58, K.61 Chain D: E.113 Ligands: SO4.4, GOL.5 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Salt bridges: A:R.35, A:K.57, A:H.58, A:K.61 Hydrogen bonds: D:E.113 Water bridges: D:E.113 SO4.4: 4 residues within 4Å: Chain A: K.57, R.60, K.61 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.57, A:R.60, A:K.61 SO4.8: 3 residues within 4Å: Chain A: K.8 Chain B: K.76, T.78 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.78 Salt bridges: B:K.76, A:K.8 SO4.9: 1 residues within 4Å: Chain B: K.29 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.29 SO4.11: 2 residues within 4Å: Chain C: A.53, R.56 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Water bridges: C:A.53 Salt bridges: C:R.56 Hydrogen bonds: A:Q.93 SO4.12: 1 residues within 4Å: Chain C: H.52 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.52 SO4.13: 7 residues within 4Å: Chain B: E.113 Chain C: R.35, K.57, H.58, K.61 Ligands: SO4.14, GOL.15 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Water bridges: B:E.113 Salt bridges: C:R.35, C:K.57, C:H.58, C:K.61 SO4.14: 4 residues within 4Å: Chain C: K.57, R.60, K.61 Ligands: SO4.13 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:K.57, C:R.60, C:K.61 SO4.18: 3 residues within 4Å: Chain C: K.8 Chain D: K.76, T.78 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.78 Salt bridges: D:K.76, C:K.8 SO4.19: 1 residues within 4Å: Chain D: K.29 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.29

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: L.39, K.42, N.43, K.54, K.57, H.58 Ligands: SO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.43, A:K.54, A:K.57, A:K.57 GOL.15: 7 residues within 4Å: Chain C: L.39, K.42, N.43, K.54, K.57, H.58 Ligands: SO4.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.43, C:K.54, C:K.57, C:K.57

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain B: D.19, D.21, D.23, T.25, E.30 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.19, B:D.21, B:D.23, B:E.30, H2O.5 CA.7: 5 residues within 4Å: Chain B: D.55, D.57, N.59, T.61, E.66 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.55, B:D.57, B:T.61, B:E.66, H2O.4 CA.16: 5 residues within 4Å: Chain D: D.19, D.21, D.23, T.25, E.30 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.19, D:D.21, D:D.23, D:E.30, H2O.12 CA.17: 5 residues within 4Å: Chain D: D.55, D.57, N.59, T.61, E.66 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.55, D:D.57, D:T.61, D:E.66, H2O.11

2 x AJV: 7-fluoro-3-(hydroxyamino)-2H-indol-2-one(Non-covalent)

AJV.10: 11 residues within 4Å: Chain A: A.83, L.86, V.87 Chain B: F.18, I.26, L.31, M.50, V.54, I.62, F.67, M.70 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.86, A:V.87, B:F.18, B:F.67 Hydrogen bonds: A:A.83 AJV.20: 11 residues within 4Å: Chain C: A.83, L.86, V.87 Chain D: F.18, I.26, L.31, M.50, V.54, I.62, F.67, M.70 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.18, D:F.67, C:L.86, C:V.87 Hydrogen bonds: C:A.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nam, Y.W. et al., Structural insights into the potency of SK channel positive modulators. Sci Rep (2017)

Release Date

2017-12-20

Peptides

Small conductance calcium-activated potassium channel protein 2: AC
Calmodulin-1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
B

B
R

D
R

Small conductance calcium-activated potassium channel protein 2

Calmodulin-1

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