SMTL ID : 1p5z.1

Structure of human dCK complexed with cytarabine and ADP-MG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.38, E.130 Ligands: ADP.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.38, A:E.130, H2O.7, H2O.7, H2O.7 MG.4: 3 residues within 4Å: Chain B: S.38, E.130 Ligands: ADP.6 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.38, B:E.130, H2O.14, H2O.14, H2O.14

2 x AR3: CYTARABINE(Non-covalent)

AR3.2: 13 residues within 4Å: Chain A: I.33, E.56, V.58, W.61, L.85, M.88, Y.89, F.99, Q.100, R.131, D.136, F.140, E.200 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.56, A:Q.100, A:R.131, A:R.131, A:D.136, A:E.200 Water bridges: A:A.34, A:E.56, A:E.56, A:R.107 pi-Stacking: A:F.140 AR3.5: 13 residues within 4Å: Chain B: I.33, E.56, V.58, W.61, L.85, M.88, Y.89, F.99, Q.100, R.131, D.136, F.140, E.200 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:E.56, B:Y.89, B:Q.100, B:R.131, B:R.131, B:D.136, B:D.136, B:E.200, B:E.200 Water bridges: B:A.34, B:K.37, B:R.107 pi-Stacking: B:F.140

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

ADP.3: 16 residues within 4Å: Chain A: N.32, A.34, A.35, G.36, K.37, S.38, T.39, E.130, R.191, L.194, R.195, V.241, E.243, D.244, F.245 Ligands: MG.1 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:N.32, A:A.34, A:A.35, A:G.36, A:K.37, A:S.38, A:T.39, A:T.39, A:L.194, A:E.243, A:F.245 Water bridges: A:K.37, A:K.37, A:K.37, A:S.38, A:T.39, A:R.197, A:R.197, A:R.197, A:R.197 Salt bridges: A:K.37 pi-Cation interactions: A:R.191 ADP.6: 16 residues within 4Å: Chain B: N.32, A.34, A.35, G.36, K.37, S.38, T.39, E.130, R.191, L.194, R.195, V.241, E.243, D.244, F.245 Ligands: MG.4 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:N.32, B:A.34, B:A.35, B:G.36, B:K.37, B:S.38, B:T.39, B:T.39, B:L.194, B:E.243, B:D.244, B:F.245 Water bridges: B:K.37, B:K.37, B:K.37, B:S.38, B:T.39, B:R.197, B:R.197, B:R.197, B:R.197 Salt bridges: B:K.37 pi-Cation interactions: B:R.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sabini, E. et al., Structure of human dCK suggests strategies to improve anticancer and antiviral therapy. Nat.Struct.Biol. (2003)

Release Date

2003-07-01

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Deoxycytidine kinase

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