SMTL ID : 2v54.1

Crystal structure of vaccinia virus thymidylate kinase bound to TDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.1: 17 residues within 4Å: Chain A: D.13, K.17, T.18, N.37, F.38, P.39, R.41, L.53, F.68, R.72, D.92, R.93, S.97, G.98, Y.101, E.142, Y.144 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.38, A:R.93 Hydrogen bonds: A:D.13, A:T.18, A:R.72, A:R.72, A:D.92, A:E.142, A:E.142 Water bridges: A:K.14, A:K.14, A:G.98, A:A.102, A:Y.144 Salt bridges: A:K.17, A:K.17, A:R.41, A:R.93, A:R.93 pi-Stacking: A:F.68 TYD.4: 16 residues within 4Å: Chain B: D.13, K.17, F.38, P.39, R.41, L.53, F.68, R.72, D.92, R.93, S.97, G.98, Y.101, Y.144 Ligands: MG.2, POP.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:R.93, B:Y.101 Hydrogen bonds: B:D.13, B:N.37, B:R.72, B:R.72 Water bridges: B:S.97, B:Y.144, B:Y.144, B:E.145 Salt bridges: B:K.17, B:K.17, B:R.41, B:R.93, B:R.93 pi-Stacking: B:F.68

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: D.13, E.142, E.145 Ligands: POP.3, TYD.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.13, B:E.145, H2O.4

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.3: 10 residues within 4Å: Chain B: L.12, D.13, K.14, S.15, G.16, K.17, T.18, E.145 Ligands: MG.2, TYD.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.14, B:S.15, B:G.16, B:K.17, B:T.18, B:T.18 Water bridges: B:T.19, B:E.145 Salt bridges: B:K.14, B:K.17, B:K.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caillat, C. et al., Crystal Structure of Poxvirus Thymidylate Kinase: An Unexpected Dimerization Has Implications for Antiviral Therapy. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2008-10-21

Peptides

THYMIDYLATE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

THYMIDYLATE KINASE

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