PDBsum entry 3f0t

Transferase

PDB id: 3f0t

Contents

Protein chains

309 a.a.

Ligands

SO4 ×6

NCV ×2

Waters ×303

References listed in PDB file

Key reference

Title

Synthesis, Crystal structure, And in vitro biological evaluation of c-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo.

Authors

M.Martić, L.Pernot, Y.Westermaier, R.Perozzo, T.G.Kraljević, S.Krištafor, S.Raić-Malić, L.Scapozza, S.Ametamey.

Ref.

Nucleosides Nucleotides Nucleic Acids, 2011, 30, 293-315.

PubMed id

21623543

Abstract

No abstract given.

Secondary reference #1

Title

Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by x-Ray crystallography.

Authors

J.Vogt, R.Perozzo, A.Pautsch, A.Prota, P.Schelling, B.Pilger, G.Folkers, L.Scapozza, G.E.Schulz.

Ref.

Proteins, 2000, 41, 545-553. [DOI no: 10.1002/1097-0134(20001201)41:4<545::AID-PROT110>3.0.CO;2-8]

PubMed id

11056041

Figure 3.
Figure 3. Structural formulae of the adenosine analogue 9-(2-(S)-hydroxypropyl)adenine (HPA) and the AMP analogue 9-(2-phosphonylmethoxyethyl)adenine (PMEA). HPA was used as a racemic mixture.

Figure 6.
Figure 6. Superposition of mutant TK[HSV1](Q125N) in complex with dT (thick solid lines, C atoms marked by small dots, hydrogen bonds are dotted) with wild-type TK[HSV1] in complex with aciclovir (thin solid lines),[19] ganciclovir (thin dotted lines)[19]and dT (thick dotted lines).[19] For sake of clarity, side chains are only drawn for TK[HSV1](Q125N):dT and TK[HSV1]:aciclovir. Water molecules and hydrogen bonds are depicted for TK[HSV1](Q125N):dT (black circles) and TK[HSV1]:aciclovir (pale circles). For aciclovir, only the location of the hydroxyl group at the 5 -OH position of dT is shown.

The above figures are reproduced from the cited reference with permission from John Wiley & Sons, Inc.

Secondary reference #2

Title

The three-Dimensional structure of thymidine kinase from herpes simplex virus type 1.

Authors

K.Wild, T.Bohner, A.Aubry, G.Folkers, G.E.Schulz.

Ref.

FEBS Lett, 1995, 368, 289-292. [DOI no: 10.1016/0014-5793(95)00680-8]

PubMed id

7628623

Figure 1.
Fig. 1. Sketch of the chain fold of thymidine kinase from Herpes simplex virus type 1. To avoid crossovers the sketch is somewhat sim- plified rendering some helix positions disputable. All ,B-strands (quad- rangles) run towards the viewer, the orientations of the helices (circles) are indicated by the arrows. Dashed lines denote chain segments that are not yet modeled. The central residues of secondary structure ele- ments bl, b2, b3, b4, b5, al, a, a3 a4, a5, a6, a7, a8, a9, al0, al 1, and a12 are 52, 79, 159, 203, 326, 67, 87, 103, 131, 72, 190, 215, 239, 292, 314, 340, and 364, respectively.

Figure 2.
Fig. 2. Stereo-view of the current a-backbone of dimeric thymidine kinase from Herpes simplex virus type 1 with numbering and the bound substrates thymidine and ATP. The dashed lines indicate regions of low density which have not yet been modeled. The chosen orientation emphasizes the planarity of the interface. The two-fold axis runs from the lefthand side in the front to the right hand side in the rear.

The above figures are reproduced from the cited reference with permission from the Federation of European Biochemical Societies

Secondary reference #3

Title

Crystal structures of the thymidine kinase from herpes simplex virus type-1 in complex with deoxythymidine and ganciclovir.

Authors

D.G.Brown, R.Visse, G.Sandhu, A.Davies, P.J.Rizkallah, C.Melitz, W.C.Summers, M.R.Sanderson.

Ref.

Nat Struct Biol, 1995, 2, 876-881.

PubMed id

7552712