SMTL ID : 2zi4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.54, E.146 Ligands: ADP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.54, A:E.146, H2O.2, H2O.2 MG.4: 3 residues within 4Å: Chain B: S.54, E.146 Ligands: ADP.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.54, B:E.146, H2O.5, H2O.6

2 x 3L1: (2S,3R,5S)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol(Non-covalent)

3L1.2: 13 residues within 4Å: Chain A: E.72, V.74, W.77, L.101, M.104, Y.105, F.115, Q.116, R.123, R.147, D.152, F.156, E.216 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.77, A:L.101 Hydrogen bonds: A:Y.105, A:Q.116, A:R.123, A:R.147, A:D.152 Water bridges: A:R.147, A:R.213 pi-Stacking: A:F.115, A:F.156, A:F.156 3L1.5: 13 residues within 4Å: Chain B: E.72, V.74, W.77, L.101, M.104, Y.105, F.115, Q.116, R.123, R.147, D.152, F.156, E.216 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.77, B:L.101 Hydrogen bonds: B:Y.105, B:Y.105, B:Q.116, B:R.123, B:R.147, B:D.152, B:D.152, B:E.216 Water bridges: B:R.147, B:R.213, B:Y.223 pi-Stacking: B:F.115, B:F.156, B:F.156

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

ADP.3: 16 residues within 4Å: Chain A: N.48, A.50, A.51, G.52, K.53, S.54, T.55, E.146, R.207, L.210, R.211, V.257, E.259, D.260, F.261 Ligands: MG.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.50, A:A.51, A:G.52, A:K.53, A:S.54, A:T.55, A:T.55, A:L.210, A:E.259, A:F.261 Water bridges: A:K.53, A:K.53, A:S.54, A:R.207, A:R.207, A:R.213, A:R.213, A:R.213, A:K.262 Salt bridges: A:K.53 pi-Cation interactions: A:R.207 ADP.6: 16 residues within 4Å: Chain B: N.48, A.50, A.51, G.52, K.53, S.54, T.55, E.146, R.207, L.210, R.211, V.257, E.259, D.260, F.261 Ligands: MG.4 22 PLIP interactions: 22 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:L.210, B:E.259, B:D.260, B:F.261 Water bridges: B:K.53, B:K.53, B:S.54, B:R.207, B:R.207, B:R.213, B:R.213, B:R.213, B:K.262 Salt bridges: B:K.53 pi-Cation interactions: B:R.207

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
A

Deoxycytidine kinase

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