SMTL ID : 2uz3.1

Crystal Structure of Thymidine Kinase with dTTP from U. urealyticum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.173, C.176, C.211, H.214 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.173, A:C.176, A:C.211, A:H.214 ZN.3: 4 residues within 4Å: Chain B: C.173, C.176, C.211, H.214 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.173, B:C.176, B:C.211, B:H.214 ZN.6: 4 residues within 4Å: Chain C: C.173, C.176, C.211, H.214 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.173, C:C.176, C:C.211, C:H.214 ZN.8: 4 residues within 4Å: Chain D: C.173, C.176, C.211, H.214 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.173, D:C.176, D:C.211, D:H.214

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

TTP.2: 22 residues within 4Å: Chain A: M.41, F.42, A.43, G.44, K.45, T.46, E.117, Q.119, F.120, L.144, K.146, N.147, F.148, F.153, S.183, R.185, I.198, V.199, K.200, I.201, G.202, Y.207 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.153, A:Y.207, A:Y.207 Hydrogen bonds: A:F.42, A:A.43, A:G.44, A:K.45, A:T.46, A:T.46, A:E.117, A:Q.119, A:F.148, A:R.185, A:I.198, A:K.200, A:G.202 Salt bridges: A:K.45, A:K.45, A:K.45 TTP.5: 26 residues within 4Å: Chain B: P.40, M.41, F.42, A.43, G.44, K.45, T.46, D.71, R.73, R.81, E.117, F.120, L.144, K.146, N.147, F.148, F.153, S.183, R.185, I.198, V.199, K.200, I.201, G.202, Y.207 Ligands: MG.4 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:L.144, B:F.153, B:Y.207, B:Y.207 Hydrogen bonds: B:F.42, B:A.43, B:G.44, B:K.45, B:T.46, B:T.46, B:R.73, B:R.73, B:R.81, B:F.148, B:R.185, B:I.198, B:K.200, B:G.202, B:Y.207 Water bridges: B:A.47 Salt bridges: B:K.45, B:K.45, B:K.45, B:R.73, B:R.73, B:R.81 TTP.7: 21 residues within 4Å: Chain C: M.41, F.42, A.43, G.44, K.45, T.46, E.117, F.120, L.144, K.146, N.147, F.148, F.153, S.183, R.185, I.198, V.199, K.200, I.201, G.202, Y.207 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:F.153, C:Y.207, C:Y.207 Hydrogen bonds: C:F.42, C:A.43, C:G.44, C:K.45, C:T.46, C:T.46, C:Q.119, C:F.148, C:R.185, C:I.198, C:K.200, C:G.202, C:Y.207 Water bridges: C:A.47, C:A.47 Salt bridges: C:K.45, C:K.45, C:K.45 pi-Stacking: C:Y.207 TTP.10: 24 residues within 4Å: Chain D: P.40, M.41, F.42, A.43, G.44, K.45, T.46, E.117, Q.119, F.120, L.144, K.146, N.147, F.148, F.153, S.183, R.185, I.198, V.199, K.200, I.201, G.202, Y.207 Ligands: MG.9 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.144, D:F.153, D:Y.207, D:Y.207 Hydrogen bonds: D:P.40, D:F.42, D:A.43, D:G.44, D:K.45, D:T.46, D:E.117, D:Q.119, D:F.148, D:R.185, D:I.198, D:K.200, D:G.202, D:Y.207 Water bridges: D:A.47, C:Y.58 Salt bridges: D:K.45, D:K.45, D:K.45

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain B: K.45, T.46 Ligands: TTP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.46 MG.9: 2 residues within 4Å: Chain D: T.46 Ligands: TTP.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.46

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

2007-05-29

Peptides

THYMIDINE KINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

THYMIDINE KINASE