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

Crystal structure of Varicella zoster virus thymidine kinase in complex with BVDU-MP and ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 9 residues within 4Å: Chain A: A.20, Y.21, G.22, I.23, G.24, K.25, T.26, T.27 Ligands: BVP.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.22, A:I.23, A:G.24, A:K.25, A:T.26, A:T.26, A:T.27 Salt bridges: A:K.25 ADP.3: 12 residues within 4Å: Chain B: A.20, Y.21, G.22, I.23, G.24, K.25, T.26, T.27, R.183, Q.300, P.302 Ligands: BVP.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.22, B:I.23, B:G.24, B:K.25, B:T.26, B:T.26, B:T.27, B:Q.300 Salt bridges: B:K.25 pi-Cation interactions: B:R.183

2 x BVP: (E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE(Non-covalent)

BVP.2: 15 residues within 4Å: Chain A: Y.21, G.22, E.48, W.53, I.62, I.65, Y.66, Q.90, F.93, H.97, R.130, A.134, S.135, F.139 Ligands: ADP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.139 Hydrogen bonds: A:G.22, A:E.48, A:Y.66, A:Q.90, A:Q.90 Water bridges: A:R.143 Salt bridges: A:K.25, A:R.130 pi-Stacking: A:F.93, A:F.139 BVP.4: 15 residues within 4Å: Chain B: Y.21, G.22, E.48, W.53, I.62, I.65, Y.66, Q.90, F.93, H.97, R.130, A.134, S.135, F.139 Ligands: ADP.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.139 Hydrogen bonds: B:G.22, B:E.48, B:Y.66, B:Q.90, B:Q.90 Salt bridges: B:K.25, B:R.130 pi-Stacking: B:F.93, B:F.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bird, L.E. et al., Crystal structure of varicella zoster virus thymidine kinase. J.Biol.Chem. (2003)

Release Date

2003-06-10

Peptides

Thymidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidine kinase

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