SMTL ID : 4g27.1

Calcium-calmodulin complexed with the calmodulin binding domain from a small conductance potassium channel splice variant and phenylurea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.36, K.58, H.59, K.62 Chain D: E.115 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.36, A:H.59 Salt bridges: A:R.36, A:K.58, A:H.59, A:K.62 SO4.5: 4 residues within 4Å: Chain A: K.9 Chain B: K.78, D.79, T.80 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.80, B:T.80 Water bridges: B:K.78, B:K.78, B:D.81, B:D.81 Salt bridges: B:K.78, A:K.9 SO4.6: 1 residues within 4Å: Chain B: R.127 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.127 SO4.8: 5 residues within 4Å: Chain B: E.115 Chain C: R.36, K.58, H.59, K.62 6 PLIP interactions: 6 interactions with chain C Water bridges: C:R.36, C:H.59 Salt bridges: C:R.36, C:K.58, C:H.59, C:K.62 SO4.12: 4 residues within 4Å: Chain C: K.9 Chain D: K.78, D.79, T.80 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain D Salt bridges: C:K.9, D:K.78 Hydrogen bonds: D:T.80, D:T.80 Water bridges: D:K.78, D:K.78, D:D.81 SO4.13: 1 residues within 4Å: Chain D: R.127 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.127

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain B: D.21, D.23, G.24, D.25, T.27, I.28, E.32 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.21, B:D.23, B:D.25, B:E.32, H2O.3 CA.3: 8 residues within 4Å: Chain B: D.57, A.58, D.59, G.60, N.61, T.63, I.64, E.68 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.57, B:D.59, B:T.63, B:E.68, H2O.3 CA.9: 7 residues within 4Å: Chain D: D.21, D.23, G.24, D.25, T.27, I.28, E.32 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.21, D:D.23, D:D.25, D:E.32, H2O.11 CA.10: 8 residues within 4Å: Chain D: D.57, A.58, D.59, G.60, N.61, T.63, I.64, E.68 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.57, D:D.59, D:T.63, D:E.68, H2O.11

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain B: K.95, Y.100, I.101, S.102, E.105, Q.136 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.95, B:S.102, B:S.102 Water bridges: B:Q.136, B:Q.136 GOL.11: 6 residues within 4Å: Chain D: K.95, Y.100, I.101, S.102, E.105, Q.136 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.95, D:S.102, D:S.102 Water bridges: D:Q.136, D:Q.136

2 x PHU: 1-phenylurea(Non-covalent)

PHU.7: 12 residues within 4Å: Chain A: A.84, L.87, V.88 Chain B: I.28, L.33, M.52, I.53, E.55, V.56, I.64, F.69, M.72 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.28, B:L.33, B:L.33, B:I.64, B:F.69, B:F.69, A:L.87 Hydrogen bonds: B:M.52, B:M.52 PHU.14: 12 residues within 4Å: Chain C: A.84, L.87, V.88 Chain D: I.28, L.33, M.52, I.53, E.55, V.56, I.64, F.69, M.72 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.28, D:L.33, D:L.33, D:I.64, D:F.69, D:F.69, C:L.87 Hydrogen bonds: D:M.52, D:M.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, M. et al., Identification of the functional binding pocket for compounds targeting small-conductance Ca(2+)-activated potassium channels. Nat Commun (2012)

Release Date

2012-09-12

Peptides

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

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