SMTL ID : 3qhw.1 (1 other biounit)

Structure of a pCDK2/CyclinA transition-state mimic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

hetero-1-1-2-mer

Ligands

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

ADP.1: 24 residues within 4Å: Chain A: I.12, G.13, E.14, G.15, T.16, Y.17, G.18, V.20, A.33, K.35, V.66, F.82, E.83, F.84, L.85, D.88, K.91, Q.133, N.134, L.136, D.147 Ligands: MG.2, MG.3, MGF.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.15, A:Y.17, A:G.18, A:E.83, A:L.85, A:D.88, A:Q.133 Water bridges: A:D.88, A:Q.133, A:N.134, A:D.147 Salt bridges: A:K.35, A:K.35

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.134, D.147 Ligands: ADP.1, MGF.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.147, H2O.5 MG.3: 4 residues within 4Å: Chain A: Y.17, D.147 Ligands: ADP.1, MGF.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.147, A:D.147, H2O.1, H2O.7

1 x MGF: TRIFLUOROMAGNESATE(Non-covalent)

MGF.4: 11 residues within 4Å: Chain A: G.15, T.16, Y.17, D.129, K.131, N.134, D.147 Chain C: T.3 Ligands: ADP.1, MG.2, MG.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.3

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

CL.5: 4 residues within 4Å: Chain A: K.131, P.132, Q.133 Chain C: P.1 Ligand excluded by PLIP

1 x DTU: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTU.6: 5 residues within 4Å: Chain B: M.18, K.21, C.22, R.70, D.134 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.134, A:E.59 Water bridges: B:K.21, B:R.70, B:D.134, A:E.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bao, Z.Q. et al., Briefly Bound to Activate: Transient Binding of a Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis. Structure (2011)

Release Date

2011-05-25

Peptides

Cell division protein kinase 2: A
Cyclin-A2: B
CDK2 substrate peptide: PKTPKKAKKL: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
J

D
L

Cell division protein kinase 2

Cyclin-A2

CDK2 substrate peptide: PKTPKKAKKL

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