SMTL ID : 2zi7.1

C4S dCK variant of dCK in complex with D-dG+UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

2 x GNG: 2'-DEOXY-GUANOSINE(Non-covalent)

GNG.1: 16 residues within 4Å: Chain A: I.49, E.72, V.74, W.77, L.101, M.104, Y.105, F.115, Q.116, R.123, R.147, D.152, F.156, L.160, R.213, E.216 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.49 Hydrogen bonds: A:E.72, A:Y.105, A:Q.116, A:Q.116, A:R.123, A:R.123, A:R.147, A:E.216 Water bridges: A:Y.105, A:R.147, A:R.211 pi-Stacking: A:F.156, A:F.156 GNG.3: 16 residues within 4Å: Chain B: I.49, E.72, W.77, L.101, M.104, Y.105, F.115, Q.116, R.123, R.147, D.152, F.156, L.160, R.213, E.216, Y.223 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.49 Hydrogen bonds: B:E.72, B:Y.105, B:Q.116, B:Q.116, B:R.123, B:R.147, B:E.216, B:E.216, B:Y.223 Water bridges: B:Y.105, B:R.147 pi-Stacking: B:F.156, B:F.156

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 14 residues within 4Å: Chain A: N.48, A.50, A.51, G.52, K.53, S.54, T.55, E.146, R.207, L.210, R.211, D.260, F.261, K.262 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.261 Hydrogen bonds: A:A.50, A:G.52, A:K.53, A:S.54, A:T.55, A:T.55, A:T.55, A:D.260, A:F.261, A:K.262, A:K.262 Water bridges: A:K.53, A:R.147, A:R.211, A:R.213 Salt bridges: A:K.53, A:R.211, A:R.211 pi-Cation interactions: A:R.207 UDP.4: 14 residues within 4Å: Chain B: N.48, A.50, A.51, G.52, K.53, S.54, T.55, E.146, R.207, L.210, R.211, D.260, F.261, K.262 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.261 Hydrogen bonds: B:A.50, B:A.51, B:G.52, B:K.53, B:S.54, B:T.55, B:T.55, B:D.260, B:D.260, B:F.261, B:K.262, B:K.262 Water bridges: B:K.53, B:K.53 Salt bridges: B:K.53, B:R.211, B:R.211 pi-Cation interactions: B:R.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sabini, E. et al., Elucidation of different binding modes of purine nucleosides to human deoxycytidine kinase. J.Med.Chem. (2008)

Release Date

2008-07-08

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Deoxycytidine kinase

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