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

Crystal Structure of Human Thymidine Kinase 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 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

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.33, D.97 Ligands: TTP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.33 MG.5: 3 residues within 4Å: Chain B: S.33, D.97 Ligands: TTP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.33 MG.8: 3 residues within 4Å: Chain C: S.33, D.97 Ligands: TTP.9 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.33, H2O.4 MG.11: 2 residues within 4Å: Chain D: S.33 Ligands: TTP.12 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.33, H2O.4

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

TTP.3: 23 residues within 4Å: Chain A: 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, T.163, R.165, V.172, E.173, V.174, I.175, G.176, Y.181 Ligands: MG.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.163, A:Y.181, A:Y.181 Hydrogen bonds: A:F.29, A:S.30, A:G.31, A:K.32, A:S.33, A:D.58, A:Q.100, A:F.128, A:R.165, A:V.172, A:V.174, A:G.176, A:Y.181 Water bridges: A:K.32, A:K.32 Salt bridges: A:K.32, A:K.32, A:K.32, A:R.60, A:R.60 pi-Stacking: A:F.133 TTP.6: 23 residues within 4Å: Chain B: 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, T.163, R.165, V.172, E.173, V.174, I.175, G.176, Y.181 Ligands: MG.5 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:L.124, B:T.163, B:Y.181, B:Y.181 Hydrogen bonds: B:F.29, B:S.30, B:G.31, B:K.32, B:S.33, B:D.58, B:Q.100, B:F.128, B:R.165, B:V.172, B:V.174, B:G.176, B:Y.181 Water bridges: B:T.34, B:T.34 Salt bridges: B:K.32, B:K.32, B:K.32, B:R.60, B:R.60 pi-Stacking: B:F.133, B:Y.181 TTP.9: 25 residues within 4Å: Chain C: P.27, M.28, F.29, S.30, G.31, K.32, S.33, D.58, R.60, E.98, Q.100, F.101, L.124, T.127, F.128, F.133, T.163, R.165, V.172, E.173, V.174, I.175, G.176, Y.181 Ligands: MG.8 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:L.124, C:F.133, C:T.163, C:Y.181, C:Y.181 Hydrogen bonds: C:F.29, C:S.30, C:G.31, C:K.32, C:S.33, C:D.58, C:Q.100, C:F.128, C:R.165, C:V.172, C:V.174, C:G.176, C:Y.181 Water bridges: C:T.34, C:L.124 Salt bridges: C:K.32, C:K.32, C:K.32, C:R.60, C:R.60 pi-Stacking: C:Y.181 TTP.12: 25 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, Q.100, F.101, L.124, T.127, F.128, F.133, T.163, R.165, V.172, E.173, V.174, I.175, G.176, Y.181 Ligands: MG.11 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:L.124, D:T.163, D:Y.181, D:Y.181 Hydrogen bonds: D:F.29, D:S.30, D:G.31, D:K.32, D:S.33, D:D.58, D:E.98, D:Q.100, D:F.128, D:R.165, D:V.172, D:V.174, D:G.176, D:Y.181 Water bridges: D:T.34 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Welin, M. et al., Structures of thymidine kinase 1 of human and mycoplasmic origin. Proc.Natl.Acad.Sci.Usa (2004)

Release Date

2004-12-14

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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