SMTL ID : 1rdq.1

Hydrolysis of ATP in the crystal of Y204A mutant of cAMP-dependent protein kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

hetero-1-1-mer

Ligands

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

PO4.1: 13 residues within 4Å: Chain A: G.52, S.53, F.54, D.166, K.168, N.171, D.184, T.201 Chain B: A.17 Ligands: MG.2, MG.3, ADP.4, ATP.5 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.53, A:N.171, A:D.184, B:A.17 Water bridges: A:K.168, A:K.168, A:N.171 Salt bridges: A:K.168

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: N.171, D.184 Ligands: PO4.1, MG.3, ADP.4, ATP.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.184, H2O.6 MG.3: 6 residues within 4Å: Chain A: F.54, D.184 Ligands: PO4.1, MG.2, ADP.4, ATP.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.184, A:D.184, H2O.2, H2O.2

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

ADP.4: 27 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: PO4.1, MG.2, MG.3, ATP.5 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.52, A:S.53, A:F.54, A:G.55, A:E.121, A:V.123, A:E.127, A:T.183, A:D.184, A:D.184, B:R.14 Water bridges: A:E.170, A:N.171, A:D.184 Salt bridges: A:K.72, A:K.72

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 30 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, D.166, K.168, E.170, N.171, L.173, T.183, D.184, F.327 Chain B: R.14, A.17 Ligands: PO4.1, MG.2, MG.3, ADP.4 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.52, A:S.53, A:F.54, A:G.55, A:E.121, A:V.123, A:E.127, A:D.166, A:D.166, A:N.171, A:T.183, A:D.184, B:R.14, B:A.17 Water bridges: A:K.168, A:K.168, A:E.170, A:N.171, A:D.184 Salt bridges: A:K.72, A:K.72, A:K.168

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6: 8 residues within 4Å: Chain A: V.15, F.18, F.100, L.152, E.155, Y.156, I.303, Y.306 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.18, A:F.100, A:E.155, A:I.303, A:Y.306 Water bridges: A:K.292

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: F.43, D.44, R.45 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.44, A:R.45, A:R.45 Water bridges: A:R.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J. et al., Crystal Structure of a cAMP-dependent Protein Kinase Mutant at 1.26A: New Insights into the Catalytic Mechanism. J.Mol.Biol. (2004)

Release Date

2004-04-13

Peptides

cAMP-dependent protein kinase, alpha-catalytic subunit: A
cAMP-dependent protein kinase inhibitor, alpha form: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
I

cAMP-dependent protein kinase, alpha-catalytic subunit

cAMP-dependent protein kinase inhibitor, alpha form

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