SMTL ID : 3qhr.2 (1 other biounit)

Structure of a pCDK2/CyclinA transition-state mimic

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

hetero-1-1-2-mer

Ligands

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

ADP.1: 23 residues within 4Å: Chain A: I.12, G.13, 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 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.17, A:G.18, A:E.83, A:L.85, A:D.88, A:K.91, A:D.147 Water bridges: A:K.35, A:Q.133, A:Q.133, A:Q.133, A:D.147 Salt bridges: A:K.35, A:K.35

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: Y.17, D.147 Ligands: ADP.1, MG.3, 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.6 MG.3: 5 residues within 4Å: Chain A: N.134, D.147 Ligands: ADP.1, MG.2, MGF.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.147, H2O.2

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: 3 residues within 4Å: Chain A: K.131, P.132, Q.133 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: K.90, M.93, D.94, E.197, R.201, R.202, A.203 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.94, A:D.94, A:E.197, A:E.197, A:R.201 GOL.7: 5 residues within 4Å: Chain A: K.58, L.68, L.69, D.70, V.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.69 Water bridges: A:L.57 GOL.8: 3 residues within 4Å: Chain B: R.16, Q.208, T.209 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.208 GOL.9: 7 residues within 4Å: Chain B: H.62, N.66, P.138, T.139, V.140, L.170, P.181 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.62, B:N.66, B:P.138, B:V.140 GOL.10: 5 residues within 4Å: Chain B: M.29, Q.32, I.35, T.36, N.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.32, B:N.37 GOL.11: 6 residues within 4Å: Chain B: G.80, K.81, T.114, Y.115, Q.119 Chain D: K.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.80, B:Q.119, D:K.9 GOL.12: 8 residues within 4Å: Chain B: Y.28, R.31, Q.32, L.72, S.73, S.74, M.75, S.76 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.28, B:S.76

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
C

B
D

C
J

D
M

Cell division protein kinase 2

Cyclin-A2

CDK2 substrate peptide: PKTPKKAKKL

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