SMTL ID : 2no7.1

C4S dCK variant of dCK in complex with L-dC+ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: N.49, A.51, A.52, G.53, K.54, S.55, T.56, R.208, R.212, E.260, D.261, F.262 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:N.49, A:A.51, A:A.52, A:G.53, A:K.54, A:S.55, A:T.56, A:T.56, A:E.260, A:F.262 Water bridges: A:K.54, A:K.54, A:R.212, A:R.214, A:R.214, A:R.214 Salt bridges: A:K.54, A:R.212, A:R.212 pi-Cation interactions: A:R.208 ADP.3: 13 residues within 4Å: Chain B: N.49, A.51, A.52, G.53, K.54, S.55, T.56, R.208, R.212, E.260, D.261, F.262, Y.266 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:A.51, B:G.53, B:K.54, B:S.55, B:T.56, B:T.56, B:D.261, B:F.262, B:Y.266, B:Y.266 Water bridges: B:K.54, B:K.54, B:S.55, B:R.208, B:R.208, B:R.208, B:R.212, B:R.212, B:R.212, B:R.214 Salt bridges: B:K.54, B:R.212, B:R.212 pi-Stacking: B:F.262 pi-Cation interactions: B:R.208

2 x LDC: 4-AMINO-1-(2-DEOXY-BETA-L-ERYTHRO-PENTOFURANOSYL)PYRIMIDIN-2(1H)-ONE(Non-covalent)

LDC.2: 15 residues within 4Å: Chain A: I.50, E.73, W.78, L.102, M.105, Y.106, F.116, Q.117, A.120, R.124, R.148, D.153, F.157, R.214, E.217 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.78, A:L.102 Hydrogen bonds: A:E.73, A:Y.106, A:Q.117, A:Q.117, A:R.148, A:D.153, A:E.217 Water bridges: A:K.54, A:R.148, A:R.214, A:Y.224 pi-Stacking: A:F.157 LDC.4: 16 residues within 4Å: Chain B: I.50, E.73, V.75, W.78, L.102, M.105, Y.106, F.116, Q.117, A.120, R.124, R.148, D.153, F.157, R.214, E.217 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.102 Hydrogen bonds: B:E.73, B:Q.117, B:R.148, B:R.148, B:D.153 Water bridges: B:E.73, B:C.121, B:R.212 pi-Stacking: B:F.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sabini, E. et al., Nonenantioselectivity Property of Human Deoxycytidine Kinase Explained by Structures of the Enzyme in Complex with l- and d-Nucleosides. J.Med.Chem. (2007)

Release Date

2007-07-03

Peptides

deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

deoxycytidine kinase

Related Entries With Identical Sequence