SMTL ID : 7ujx.1

Structure of cAMP-dependent protein kinase using a MD-MX procedure, produced using 2.4 Angstrom data

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 26 residues within 4Å: Chain A: L.49, G.50, T.51, G.52, S.53, F.54, G.55, V.57, A.70, K.72, V.104, M.120, E.121, Y.122, V.123, E.127, E.170, N.171, L.173, T.183, D.184, F.327 Chain B: R.14 Ligands: PO4.2, MG.3, MG.4 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.54, A:G.55, A:E.121, A:V.123, A:E.127, A:E.127, A:T.183, A:D.184, B:R.14 Water bridges: A:G.52, A:G.52, A:S.53, A:K.72, A:D.184, A:G.186, B:R.14 Salt bridges: A:K.72, A:K.72

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

PO4.2: 13 residues within 4Å: Chain A: S.53, F.54, D.166, K.168, N.171, D.184, F.187, T.201 Chain B: N.16, A.17 Ligands: ADP.1, MG.3, MG.4 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.53, A:S.53, A:D.166, A:N.171, B:A.17 Water bridges: A:K.168, A:K.168, A:G.186 Salt bridges: A:K.168 PO4.5: 7 residues within 4Å: Chain A: E.155, H.158, K.217, W.221, G.282, G.287, V.288 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.221, A:G.282 Water bridges: A:K.217, A:K.217, A:K.217, A:G.282, A:V.288, A:V.288 Salt bridges: A:H.158, A:K.217

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 8 residues within 4Å: Chain A: F.54, K.72, D.166, D.184, G.186 Ligands: ADP.1, PO4.2, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.184, A:D.184, H2O.1, H2O.3 MG.4: 5 residues within 4Å: Chain A: N.171, D.184 Ligands: ADP.1, PO4.2, MG.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.184, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wych, D.C. et al., Molecular-dynamics simulation methods for macromolecular crystallography. Acta Crystallogr D Struct Biol (2023)

Release Date

2022-12-07

Peptides

cAMP-dependent protein kinase catalytic subunit alpha: A
Peptide from cAMP-dependent protein kinase inhibitor alpha: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
I

cAMP-dependent protein kinase catalytic subunit alpha

Peptide from cAMP-dependent protein kinase inhibitor alpha

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