SMTL ID : 3qeo.1

S74E-R104M-D133A dCK variant in complex with L-deoxythymidine and UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 13 residues within 4Å: Chain A: 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 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.261 Hydrogen bonds: A:A.50, A:A.51, 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.211 Salt bridges: A:K.53, A:R.211, A:R.211 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 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:A.50, B:A.51, B:G.52, B:K.53, B:S.54, B:T.55, B:T.55, B:T.55, B:E.146, B:D.260, B:F.261, B:K.262 Water bridges: B:R.207, B:R.211, B:R.211, B:R.211, B:K.262 Salt bridges: B:K.53, B:R.211, B:R.211 pi-Stacking: B:F.261 pi-Cation interactions: B:R.207, B:K.262

2 x LLT: L-deoxythymidine(Non-covalent)

LLT.2: 11 residues within 4Å: Chain A: E.72, V.74, L.101, M.104, Y.105, F.115, Q.116, R.147, F.156, L.160, E.216 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.74, A:L.101 Hydrogen bonds: A:Y.105, A:Q.116, A:Q.116, A:E.216, A:E.216 Water bridges: A:Y.223 pi-Stacking: A:F.115 LLT.4: 8 residues within 4Å: Chain B: E.72, V.74, L.101, Y.105, F.115, Q.116, F.156, L.160 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.74, B:F.156 Hydrogen bonds: B:Q.116, B:Q.116 pi-Stacking: B:F.115, B:F.156

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