SMTL ID : 2no1.2 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: N.49, A.51, A.52, G.53, K.54, S.55, T.56, R.208, L.211, R.212, E.260, D.261, F.262 Chain C: D.261, F.262 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain C 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, C:D.261 Water bridges: A:K.54, A:K.54, A:R.212, A:R.212 Salt bridges: A:K.54, A:R.212, A:R.212 pi-Cation interactions: A:R.208 pi-Stacking: C:F.262 ADP.3: 15 residues within 4Å: Chain B: N.49, A.51, A.52, G.53, K.54, S.55, T.56, R.208, L.211, R.212, E.260, D.261, F.262 Chain D: D.261, F.262 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:N.49, B:A.51, B:A.52, B:G.53, B:K.54, B:S.55, B:T.56, B:T.56, B:E.260, B:D.261, B:F.262, D:D.261 Water bridges: B:K.54, B:K.54, B:S.55, B:R.212 Salt bridges: B:K.54, B:R.212, B:R.212 pi-Cation interactions: B:R.208 pi-Stacking: D:F.262 ADP.5: 14 residues within 4Å: Chain A: D.261, K.263 Chain C: A.51, A.52, G.53, K.54, S.55, T.56, R.208, R.212, E.260, D.261, F.262, Y.266 23 PLIP interactions: 19 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:N.49, C:A.51, C:G.53, C:K.54, C:S.55, C:T.56, C:T.56, C:E.260, C:D.261, C:F.262, C:Y.266, A:D.261 Water bridges: C:K.54, C:R.208, C:R.208, A:K.263, A:K.263 Salt bridges: C:K.54, C:R.212, C:R.212, A:K.263 pi-Stacking: C:F.262 pi-Cation interactions: C:R.208 ADP.7: 14 residues within 4Å: Chain B: D.261, K.263 Chain D: A.51, A.52, G.53, K.54, S.55, T.56, R.208, R.212, E.260, D.261, F.262, Y.266 21 PLIP interactions: 17 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:N.49, D:A.51, D:G.53, D:K.54, D:S.55, D:T.56, D:T.56, D:E.260, D:F.262, B:D.261 Water bridges: D:K.54, D:R.208, D:R.208, B:K.263, B:K.263 Salt bridges: D:K.54, D:R.212, D:R.212, B:K.263 pi-Stacking: D:F.262 pi-Cation interactions: D:R.208

4 x DCZ: 2'-DEOXYCYTIDINE(Non-covalent)

DCZ.2: 14 residues within 4Å: Chain A: I.50, E.73, V.75, W.78, L.102, M.105, Y.106, F.116, Q.117, R.148, D.153, F.157, R.214, E.217 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.50, A:W.78, A:F.157 Hydrogen bonds: A:E.73, A:Y.106, A:Y.106, A:Q.117, A:R.148, A:D.153, A:D.153, A:E.217 Water bridges: A:K.54, A:R.148, A:R.214 pi-Stacking: A:F.157 DCZ.4: 14 residues within 4Å: Chain B: I.50, E.73, V.75, W.78, L.102, M.105, Y.106, F.116, Q.117, R.148, D.153, F.157, R.214, E.217 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.50, B:W.78, B:F.157 Hydrogen bonds: B:E.73, B:Y.106, B:Q.117, B:R.148, B:D.153 Water bridges: B:K.54, B:E.73, B:R.148, B:R.214 pi-Stacking: B:F.157 DCZ.6: 14 residues within 4Å: Chain C: I.50, E.73, V.75, W.78, L.102, M.105, Y.106, F.116, Q.117, R.148, D.153, F.157, R.214, E.217 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.50, C:F.157 Hydrogen bonds: C:E.73, C:Y.106, C:Q.117, C:R.148, C:D.153 Water bridges: C:R.148 pi-Stacking: C:F.157 DCZ.8: 14 residues within 4Å: Chain D: I.50, E.73, V.75, W.78, L.102, M.105, Y.106, F.116, Q.117, R.148, D.153, F.157, R.214, E.217 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.50, D:F.157 Hydrogen bonds: D:E.73, D:Y.106, D:Y.106, D:Q.117, D:R.148, D:D.153, D:D.153, D:E.217 Water bridges: D:R.148 pi-Stacking: D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

deoxycytidine kinase

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