SMTL ID : 3qen.1

S74E dCK in complex with 5-bromodeoxycytidine and UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 11 residues within 4Å: Chain A: A.50, A.51, G.52, K.53, S.54, T.55, R.207, R.211, D.260, F.261, K.262 20 PLIP interactions: 20 interactions with chain A 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:D.260, A:F.261, A:K.262, A:K.262 Water bridges: A:K.53, A:S.54, A:R.147 Salt bridges: A:K.53, A:R.211, A:R.211 pi-Stacking: A:F.261 pi-Cation interactions: A:R.207 UDP.3: 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:G.52, B:K.53, B:S.54, B:T.55, B:T.55, B:T.55, B:R.207, B:D.260, B:F.261, 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, B:K.262

2 x 5BT: 5-bromo-2'-deoxycytidine(Non-covalent)

5BT.2: 14 residues within 4Å: Chain A: E.72, V.74, M.104, Y.105, F.115, Q.116, R.123, R.147, D.152, F.156, R.213, E.216, I.219, Y.223 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.156 Hydrogen bonds: A:Q.116, A:D.152, A:R.213, A:E.216 Water bridges: A:C.120 pi-Stacking: A:F.156 Halogen bonds: A:E.72, A:R.123 5BT.4: 15 residues within 4Å: Chain B: I.49, E.72, V.74, L.101, M.104, Y.105, F.115, Q.116, R.123, R.147, D.152, F.156, E.216, I.219, Y.223 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.49, B:F.156 Hydrogen bonds: B:Q.116, B:D.152, B:D.152, B:Y.223 Water bridges: B:R.147 pi-Stacking: B:F.156 Halogen bonds: B:E.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hazra, S. et al., Post-translational phosphorylation of serine 74 of human deoxycytidine kinase favors the enzyme adopting the open conformation making it competent for nucleoside binding and release. Biochemistry (2011)

Release Date

2011-03-16

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deoxycytidine kinase

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