SMTL ID : 3kfx.2 (1 other biounit)

Human dCK complex with 5-Me dC and ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: N.48, A.50, A.51, G.52, K.53, S.54, T.55, R.207, R.211, V.257, E.259, D.260, F.261, Y.265 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:N.48, A:A.50, A:G.52, A:K.53, A:S.54, A:T.55, A:T.55, A:F.261, A:Y.265 Water bridges: A:K.53, A:S.54, A:S.54, A:R.211, A:R.213, A:R.213 Salt bridges: A:K.53, A:R.211, A:R.211 pi-Stacking: A:F.261 pi-Cation interactions: A:R.207 ADP.3: 13 residues within 4Å: Chain B: N.48, A.50, A.51, G.52, K.53, S.54, T.55, R.207, L.210, R.211, E.259, D.260, F.261 19 PLIP interactions: 19 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:E.259, B:F.261 Water bridges: B:K.53, B:K.53, B:S.54, B:R.211, B:R.213, B:R.213 Salt bridges: B:K.53, B:R.211, B:R.211 pi-Cation interactions: B:R.207 ADP.5: 14 residues within 4Å: Chain C: N.48, A.50, A.51, G.52, K.53, S.54, T.55, R.207, R.211, V.257, E.259, D.260, F.261, Y.265 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:N.48, C:A.50, C:G.52, C:K.53, C:S.54, C:T.55, C:T.55, C:D.260, C:F.261, C:Y.265, C:Y.265 Water bridges: C:K.53, C:S.54, C:S.54, C:R.211, C:R.213, C:R.213 Salt bridges: C:K.53, C:R.211, C:R.211 pi-Stacking: C:F.261 pi-Cation interactions: C:R.207 ADP.7: 13 residues within 4Å: Chain D: N.48, A.50, A.51, G.52, K.53, S.54, T.55, R.207, L.210, R.211, E.259, D.260, F.261 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:A.50, D:A.51, D:G.52, D:K.53, D:S.54, D:T.55, D:T.55, D:E.259, D:F.261 Water bridges: D:K.53, D:K.53, D:S.54, D:R.211, D:R.211, D:R.213 Salt bridges: D:K.53, D:R.211, D:R.211 pi-Cation interactions: D:R.207

4 x MCY: 5-METHYL-2'-DEOXYCYTIDINE(Non-covalent)

MCY.2: 14 residues within 4Å: Chain A: I.49, E.72, W.77, L.101, M.104, Y.105, F.115, Q.116, R.123, R.147, D.152, F.156, R.213, E.216 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.49, A:W.77, A:F.156 Hydrogen bonds: A:E.72, A:Y.105, A:Y.105, A:Q.116, A:R.147, A:D.152, A:D.152, A:E.216 Water bridges: A:C.120, A:R.147, A:R.211, A:Y.223 pi-Stacking: A:F.156 MCY.4: 15 residues within 4Å: Chain B: 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, R.213, E.216 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.49, B:W.77, B:W.77, B:F.156 Hydrogen bonds: B:E.72, B:Y.105, B:Q.116, B:R.147, B:D.152 Water bridges: B:K.53, B:R.147, B:R.211, B:R.213 pi-Stacking: B:F.156 MCY.6: 14 residues within 4Å: Chain C: I.49, E.72, W.77, L.101, M.104, Y.105, F.115, Q.116, R.123, R.147, D.152, F.156, R.213, E.216 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.49, C:W.77, C:F.156 Hydrogen bonds: C:E.72, C:Y.105, C:Q.116, C:R.147, C:D.152 Water bridges: C:E.72, C:C.120, C:R.147, C:R.211 pi-Stacking: C:F.156 MCY.8: 15 residues within 4Å: Chain D: 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, R.213, E.216 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.49, D:W.77, D:W.77, D:F.156 Hydrogen bonds: D:E.72, D:Y.105, D:Y.105, D:Q.116, D:R.147, D:D.152, D:D.152, D:E.216 Water bridges: D:K.53, D:R.147, D:R.211, D:R.213 pi-Stacking: D:F.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hazra, S. et al., Structural and kinetic characterization of human deoxycytidine kinase variants able to phosphorylate 5-substituted deoxycytidine and thymidine analogues . Biochemistry (2010)

Release Date

2010-09-15

Peptides

Deoxycytidine kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Deoxycytidine kinase

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