SMTL ID : 2wvj.2 (1 other biounit)

Mutation of Thr163 to Ser in Human Thymidine Kinase Shifts the Specificity from Thymidine towards the Nucleoside Analogue Azidothymidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 24 residues within 4Å: Chain A: M.28, F.29, S.30, G.31, K.32, S.33, D.58, R.60, D.97, E.98, Q.100, F.101, L.124, T.127, F.128, F.133, S.163, R.165, V.172, E.173, V.174, I.175, G.176, Y.181 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:L.124, A:Y.181, A:Y.181 Hydrogen bonds: A:F.29, A:S.30, A:S.30, A:G.31, A:K.32, A:S.33, A:S.33, A:S.33, A:D.58, A:E.98, A:Q.100, A:F.128, A:R.165, A:V.172, A:V.174, A:Y.181 Water bridges: A:E.98 Salt bridges: A:K.32, A:K.32, A:K.32, A:R.60 pi-Stacking: A:F.133, A:Y.181 TTP.3: 24 residues within 4Å: Chain B: M.28, F.29, S.30, G.31, K.32, S.33, D.58, R.60, D.97, E.98, Q.100, F.101, L.124, T.127, F.128, F.133, S.163, R.165, V.172, E.173, V.174, I.175, G.176, Y.181 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:L.124, B:Y.181, B:Y.181 Hydrogen bonds: B:F.29, B:S.30, B:S.30, B:G.31, B:K.32, B:S.33, B:S.33, B:D.58, B:R.60, B:Q.100, B:L.124, B:F.128, B:R.165, B:V.172, B:V.174, B:G.176, B:Y.181 Water bridges: B:T.34, B:E.98 Salt bridges: B:K.32, B:K.32, B:K.32 pi-Stacking: B:F.133, B:Y.181 TTP.5: 23 residues within 4Å: Chain C: M.28, F.29, S.30, G.31, K.32, S.33, D.58, R.60, E.98, F.101, L.124, T.127, F.128, F.133, S.163, R.165, V.172, E.173, V.174, I.175, G.176, Y.181 Ligands: MG.6 32 PLIP interactions: 32 interactions with chain C Hydrophobic interactions: C:L.124, C:Y.181, C:Y.181 Hydrogen bonds: C:F.29, C:S.30, C:G.31, C:K.32, C:S.33, C:S.33, C:D.58, C:R.60, C:E.98, C:F.128, C:R.165, C:V.172, C:V.174, C:G.176, C:Y.181 Water bridges: C:F.29, C:S.33, C:S.33, C:S.33, C:T.34, C:R.60, C:R.60, C:Q.100 Salt bridges: C:K.32, C:K.32, C:K.32, C:R.60, C:R.60 pi-Stacking: C:F.133 TTP.8: 24 residues within 4Å: Chain D: P.27, M.28, F.29, S.30, G.31, K.32, S.33, D.58, R.60, E.98, F.101, L.124, T.127, F.128, F.133, S.163, R.165, V.172, E.173, V.174, I.175, G.176, Y.181 Ligands: MG.9 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:L.124, D:Y.181, D:Y.181 Hydrogen bonds: D:P.27, D:F.29, D:S.30, D:G.31, D:K.32, D:S.33, D:D.58, D:Q.100, D:F.128, D:R.165, D:V.172, D:V.174, D:G.176, D:Y.181 Water bridges: D:S.33, D:T.34, D:R.60 Salt bridges: D:K.32, D:K.32, D:K.32, D:R.60, D:R.60 pi-Stacking: D:F.133, D:Y.181

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.153, C.156, C.185, C.188 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.153, A:C.156, A:C.185, A:C.188 ZN.4: 4 residues within 4Å: Chain B: C.153, C.156, C.185, C.188 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.153, B:C.156, B:C.185, B:C.188 ZN.7: 4 residues within 4Å: Chain C: C.153, C.156, C.185, C.188 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.153, C:C.156, C:C.185, C:C.188 ZN.10: 4 residues within 4Å: Chain D: C.153, C.156, C.185, C.188 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.153, D:C.156, D:C.185, D:C.188

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain C: S.33 Ligands: TTP.5 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.33, H2O.10, H2O.13 MG.9: 2 residues within 4Å: Chain D: S.33 Ligands: TTP.8 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.33, H2O.16, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skovgaard, T. et al., Comparative Active-Site Mutation Study of Human and Caenorhabditis Elegans Thymidine Kinase 1. FEBS J. (2012)

Release Date

2009-10-27

Peptides

THYMIDINE KINASE, CYTOSOLIC: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

THYMIDINE KINASE, CYTOSOLIC

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