SMTL ID : 4i3z.1 (1 other biounit)

Structure of pCDK2/CyclinA bound to ADP and 2 Magnesium ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: I.10, G.11, V.18, A.31, K.33, V.64, F.80, E.81, F.82, L.83, D.86, K.89, Q.131, N.132, L.134, D.145 Ligands: MG.2, MG.3, GOL.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.81, A:L.83, A:D.86, A:K.89, A:D.145 Water bridges: A:K.33, A:Q.131, A:Q.131, A:N.132, A:D.145, A:D.145 Salt bridges: A:K.33, A:K.33

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.132, D.145 Ligands: ADP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.145, H2O.1, H2O.1 MG.3: 2 residues within 4Å: Chain A: D.145 Ligands: ADP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.145, A:D.145, H2O.1, H2O.1, H2O.1

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: I.209, D.210, F.213, R.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.210, A:D.210, A:R.217 GOL.5: 5 residues within 4Å: Chain A: F.4, N.23, E.28, V.30, D.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.23, A:D.68, A:D.68 Water bridges: A:T.26 GOL.6: 5 residues within 4Å: Chain A: D.86, K.88, K.89, Q.131 Ligands: ADP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.86, A:K.88, A:K.89 GOL.8: 3 residues within 4Å: Chain B: E.50, Y.51, E.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.50, B:Y.51 GOL.9: 8 residues within 4Å: Chain B: Y.25, R.28, Q.29, P.30, L.69, S.70, M.72, S.73 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.25, B:R.28, B:Q.29, B:S.73

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain A: K.129, P.130, Q.131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jacobsen, D.M. et al., Price To Be Paid for Two-Metal Catalysis: Magnesium Ions That Accelerate Chemistry Unavoidably Limit Product Release from a Protein Kinase. J.Am.Chem.Soc. (2012)

Release Date

2012-12-26

Peptides

Cyclin-dependent kinase 2: A
Cyclin-A2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cyclin-dependent kinase 2

Cyclin-A2

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