SMTL ID : 2zi3.1

C4S-E247A dCK variant of dCK in complex with D-dA+ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: N.48, A.50, A.51, G.52, K.53, S.54, T.55, R.207, R.211, E.259, D.260, F.261 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.48, A:A.50, A:A.51, A:G.52, A:K.53, A:S.54, A:T.55, A:T.55, A:E.259, A:F.261 Water bridges: A:K.53, A:S.54, A:E.72, A:R.213 Salt bridges: A:K.53, A:R.211, A:R.211 pi-Cation interactions: A:R.207 ADP.3: 13 residues within 4Å: Chain B: 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 16 PLIP interactions: 16 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:R.207, B:E.259, B:D.260, B:F.261 Salt bridges: B:K.53, B:R.211, B:R.211 pi-Stacking: B:F.261 pi-Cation interactions: B:R.207

2 x 3D1: (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol(Non-covalent)

3D1.2: 13 residues within 4Å: Chain A: I.49, E.72, W.77, L.101, Y.105, F.115, Q.116, R.123, R.147, D.152, F.156, R.213, E.216 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.49 Hydrogen bonds: A:E.72, A:Y.105, A:Q.116, A:R.123, A:R.147, A:D.152, A:D.152, A:E.216 Water bridges: A:Y.223 pi-Stacking: A:F.156, A:F.156 3D1.4: 14 residues within 4Å: Chain B: I.49, E.72, V.74, W.77, L.101, 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 B Hydrophobic interactions: B:I.49 Hydrogen bonds: B:E.72, B:Q.116, B:Q.116, B:R.123, B:R.147, B:D.152, B:E.216, B:E.216 Water bridges: B:C.120 pi-Stacking: B:F.115, B:F.156, B:F.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sabini, E. et al., Structural basis for substrate promiscuity of dCK. J.Mol.Biol. (2008)

Release Date

2008-04-22

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deoxycytidine kinase

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