SMTL ID : 2wel.1

Crystal structure of SU6656-bound calcium/calmodulin-dependent protein kinase II delta in complex with calmodulin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x K88: (3Z)-N,N-DIMETHYL-2-OXO-3-(4,5,6,7-TETRAHYDRO-1H-INDOL-2-YLMETHYLIDENE)-2,3-DIHYDRO-1H-INDOLE-5-SULFONAMIDE(Non-covalent)

K88.1: 12 residues within 4Å: Chain A: L.12, V.20, A.33, K.35, F.82, D.83, L.84, V.85, A.148, D.149 Ligands: EDO.2, EDO.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.12, A:L.12, A:F.82, A:F.82 Hydrogen bonds: A:D.83, A:V.85, A:V.85 Salt bridges: A:D.149

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: G.88, L.135 Ligands: K88.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.89 EDO.3: 7 residues within 4Å: Chain A: E.53, C.57, F.82, A.148, D.149, F.150 Ligands: K88.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.53, A:D.149, A:F.150 EDO.4: 3 residues within 4Å: Chain A: F.91, E.132, Y.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.132 EDO.5: 5 residues within 4Å: Chain A: H.47, E.51, S.73, H.78 Ligands: PO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.73 Water bridges: A:H.78 EDO.6: 5 residues within 4Å: Chain A: Y.6, K.25, Y.32, H.69 Ligands: PO4.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.6, A:Y.6 Water bridges: A:H.69 EDO.7: 5 residues within 4Å: Chain A: Y.197, P.205, Y.223, D.224, P.226 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.205, A:D.224, A:D.224 Water bridges: A:D.224, A:D.224

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 7 residues within 4Å: Chain A: T.39, H.47, S.73, E.74, F.77, H.78 Ligands: EDO.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.39, A:T.39, A:E.74 Water bridges: A:G.76 Salt bridges: A:H.47, A:H.78 PO4.9: 4 residues within 4Å: Chain A: K.61, R.67, H.69 Ligands: EDO.6 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.67, A:H.69 Salt bridges: A:K.61, A:R.67, A:H.69

4 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain B: D.22, D.24, D.26, T.28, E.33 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.22, B:D.24, B:D.26, B:E.33, H2O.13 CA.11: 5 residues within 4Å: Chain B: D.58, D.60, N.62, T.64, E.69 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.58, B:D.60, B:T.64, B:E.69, H2O.14 CA.12: 5 residues within 4Å: Chain B: D.95, D.97, N.99, Y.101, E.106 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.95, B:D.97, B:Y.101, B:E.106, H2O.16 CA.13: 5 residues within 4Å: Chain B: D.131, D.133, D.135, Q.137, E.142 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.131, B:Q.137, B:E.142, B:E.142, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rellos, P. et al., Structure of the Camkiidelta/Calmodulin Complex Reveals the Molecular Mechanism of Camkii Kinase Activation. Plos Biol. (2010)

Release Date

2009-04-14

Peptides

CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN: A
CALMODULIN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN

CALMODULIN

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