SMTL ID : 3hx4.1

Crystal structure of CDPK1 of Toxoplasma gondii, TGME49_101440, in presence of calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.416, D.418, N.420, Y.422, E.424, E.427 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.416, A:D.418, A:Y.422, A:E.424, A:E.427 CA.2: 5 residues within 4Å: Chain A: D.369, N.371, D.373, Q.375, E.380 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.369, A:D.373, A:Q.375, A:E.380, H2O.1 CA.3: 5 residues within 4Å: Chain A: D.452, D.454, S.456, K.458, E.463 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.452, A:D.454, A:S.456, A:K.458, H2O.4 CA.4: 5 residues within 4Å: Chain A: D.486, N.488, D.490, E.492, E.497 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.486, A:D.490, A:E.492, A:E.497, H2O.4

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.5: 16 residues within 4Å: Chain A: L.58, K.60, S.62, E.65, V.66, A.79, K.81, E.130, V.131, Y.132, E.136, L.182, I.195, D.196 Ligands: SO4.7, GOL.11 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.60, A:S.62, A:K.81, A:E.130, A:Y.132, A:E.136 Salt bridges: A:K.81

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

SO4.6: 5 residues within 4Å: Chain A: R.174, M.209, K.210, D.211, Y.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.210, A:D.211, A:Y.228 Water bridges: A:R.174, A:R.174 Salt bridges: A:R.174 SO4.7: 3 residues within 4Å: Chain A: D.175, K.177 Ligands: ANP.5 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.177, A:K.177, A:D.196 Salt bridges: A:K.177 SO4.8: 3 residues within 4Å: Chain A: D.474, S.475, E.476 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.475, A:E.476 SO4.9: 4 residues within 4Å: Chain A: L.33, H.34, K.339, K.419 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.339, A:K.419 SO4.10: 3 residues within 4Å: Chain A: T.133, S.185, K.186 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.133, A:T.133, A:K.186 Salt bridges: A:K.186

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 10 residues within 4Å: Chain A: L.58, G.59, K.60, G.61, S.62, F.63, G.64, E.65, V.66 Ligands: ANP.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.59, A:G.61, A:G.64, A:E.65, A:E.65, A:V.66, A:V.66 GOL.12: 3 residues within 4Å: Chain A: S.279, E.280, S.281 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.280, A:S.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wernimont, A.K. et al., Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium. Nat.Struct.Mol.Biol. (2010)

Release Date

2009-07-21

Peptides

Calmodulin-domain protein kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Calmodulin-domain protein kinase 1