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

Structure of a pCDK2/CyclinA transition-state mimic

Coordinates

PDB Format Compare

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

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: K.107, D.258, D.260, P.286, F.287, Q.289, D.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.107, A:D.258, A:D.290, A:D.290 GOL.7: 7 residues within 4Å: Chain A: T.160, Y.161, T.162, H.163, E.164 Chain B: I.99, Y.100 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.163, B:Y.100 Water bridges: A:Y.161, A:K.180 GOL.8: 7 residues within 4Å: Chain A: G.1, F.6, N.25, E.30, V.32, D.70 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.25, A:E.30, A:E.30, A:D.70 GOL.9: 3 residues within 4Å: Chain A: G.1, D.70 Ligands: GOL.8 No protein-ligand interaction detected (PLIP) GOL.10: 6 residues within 4Å: Chain B: H.62, N.66, P.138, T.139, V.140, L.170 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.62, B:N.66, B:N.66, B:V.140 GOL.11: 7 residues within 4Å: Chain B: Y.28, R.31, Q.32, L.72, S.73, S.74, S.76 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.28, B:Q.32, B:S.76 GOL.12: 7 residues within 4Å: Chain B: N.37, S.38, A.41, D.172, H.233, A.234, Q.235 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.172, B:Q.235 Water bridges: B:N.37, B:A.173, B:A.173, B:D.174 GOL.13: 4 residues within 4Å: Chain B: T.13, R.16, Q.208, T.209 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.12 Water bridges: B:R.16, B:R.16 GOL.14: 6 residues within 4Å: Chain B: G.80, K.81, T.114, Y.115, Q.119 Chain D: K.9 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Q.119, B:Q.119, D:K.9, D:K.9 Water bridges: B:Y.115 GOL.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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
K

D
L

Cell division protein kinase 2

Cyclin-A2

CDK2 substrate peptide: PKTPKKAKKL

Related Entries With Identical Sequence