SMTL ID : 1p60.2 (2 other biounits)

Structure of human dCK complexed with 2'-Deoxycytidine and ADP, Space group C 2 2 21

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: N.32, A.34, A.35, G.36, K.37, S.38, T.39, R.191, L.194, R.195, E.243, D.244, F.245 Chain C: D.244, F.245 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:A.34, A:G.36, A:K.37, A:S.38, A:T.39, A:T.39, A:L.194, A:E.243, A:F.245, C:D.244 Water bridges: A:K.37, A:K.37, A:R.195, A:R.195, A:E.243 Salt bridges: A:K.37, A:R.195, A:R.195 pi-Cation interactions: A:R.191 pi-Stacking: C:F.245, C:F.245 ADP.3: 15 residues within 4Å: Chain B: N.32, A.34, A.35, G.36, K.37, S.38, T.39, R.191, L.194, R.195, E.243, D.244, F.245 Chain D: D.244, F.245 22 PLIP interactions: 19 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:A.34, B:G.36, B:K.37, B:S.38, B:T.39, B:T.39, B:L.194, B:E.243, B:D.244, B:F.245, D:D.244 Water bridges: B:K.37, B:K.37, B:R.195, B:R.195, B:E.243 Salt bridges: B:K.37, B:R.195, B:R.195 pi-Cation interactions: B:R.191 pi-Stacking: D:F.245, D:F.245 ADP.5: 16 residues within 4Å: Chain A: D.244, K.246 Chain C: N.32, A.34, A.35, G.36, K.37, S.38, T.39, R.191, R.195, V.241, E.243, D.244, F.245, Y.249 24 PLIP interactions: 22 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.32, C:A.34, C:A.35, C:G.36, C:K.37, C:S.38, C:T.39, C:T.39, C:E.243, C:D.244, C:F.245, A:D.244 Water bridges: C:K.37, C:K.37, C:S.38, C:S.38, C:R.195, C:R.197 Salt bridges: C:K.37, C:R.195, C:R.195, A:K.246 pi-Stacking: C:F.245 pi-Cation interactions: C:R.191 ADP.7: 16 residues within 4Å: Chain B: D.244, K.246 Chain D: N.32, A.34, A.35, G.36, K.37, S.38, T.39, R.191, R.195, V.241, E.243, D.244, F.245, Y.249 23 PLIP interactions: 21 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:N.32, D:A.34, D:A.35, D:G.36, D:K.37, D:S.38, D:T.39, D:T.39, D:E.243, D:F.245, B:D.244 Water bridges: D:K.37, D:K.37, D:S.38, D:S.38, D:R.195, D:R.197 Salt bridges: D:K.37, D:R.195, D:R.195, B:K.246 pi-Stacking: D:F.245 pi-Cation interactions: D:R.191

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

DCZ.2: 13 residues within 4Å: Chain A: I.33, E.56, W.61, L.85, M.88, Y.89, F.99, Q.100, R.131, D.136, F.140, R.197, E.200 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.33, A:W.61 Hydrogen bonds: A:E.56, A:Y.89, A:Y.89, A:Q.100, A:R.131, A:D.136, A:D.136, A:E.200 Water bridges: A:K.37, A:R.131, A:R.197, A:Y.207 pi-Stacking: A:F.140 DCZ.4: 13 residues within 4Å: Chain B: I.33, E.56, W.61, L.85, M.88, Y.89, F.99, Q.100, R.131, D.136, F.140, R.197, E.200 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.33, B:W.61 Hydrogen bonds: B:E.56, B:Y.89, B:Q.100, B:R.131, B:D.136 Water bridges: B:K.37, B:R.131, B:R.197 pi-Stacking: B:F.140 DCZ.6: 14 residues within 4Å: Chain C: I.33, E.56, V.58, W.61, L.85, M.88, Y.89, F.99, Q.100, R.131, D.136, F.140, R.197, E.200 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.33 Hydrogen bonds: C:E.56, C:Y.89, C:Q.100, C:R.131, C:D.136 Water bridges: C:E.56, C:R.131, C:R.197 pi-Stacking: C:F.140 DCZ.8: 14 residues within 4Å: Chain D: I.33, E.56, V.58, W.61, L.85, M.88, Y.89, F.99, Q.100, R.131, D.136, F.140, R.197, E.200 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.33 Hydrogen bonds: D:E.56, D:Y.89, D:Y.89, D:Q.100, D:R.131, D:D.136, D:D.136, D:E.200 Water bridges: D:R.131, D:R.197 pi-Stacking: D:F.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sabini, E. et al., Structure of human dCK suggests strategies to improve anticancer and antiviral therapy. Nat.Struct.Biol. (2003)

Release Date

2003-07-01

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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