SMTL ID : 2w0s.1 (1 other biounit)

Crystal structure of vaccinia virus thymidylate kinase bound to brivudin-5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.18, N.37, D.92 Ligands: BVP.3, SO4.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.18 MG.2: 4 residues within 4Å: Chain A: D.13, E.142, E.145 Ligands: BVP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.13, A:E.145, BVP.3 MG.5: 5 residues within 4Å: Chain B: T.18, N.37, D.92 Ligands: BVP.7, SO4.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.92 MG.6: 4 residues within 4Å: Chain B: D.13, E.142, E.145 Ligands: BVP.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.13, B:E.145

3 x BVP: (E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE(Non-covalent)

BVP.3: 18 residues within 4Å: Chain A: D.13, F.38, R.41, L.53, V.64, N.65, F.68, R.72, R.93, S.97, G.98, Y.101, A.102, K.105, E.142, Y.144 Ligands: MG.1, MG.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.68, A:Y.101, A:Y.101 Hydrogen bonds: A:R.72, A:R.72, A:Y.101, A:E.142 Salt bridges: A:K.17, A:R.41, A:R.93 pi-Stacking: A:F.68 Halogen bonds: A:N.65 BVP.7: 19 residues within 4Å: Chain B: D.13, F.38, P.39, R.41, L.53, V.64, N.65, F.68, R.72, R.93, S.97, G.98, Y.101, A.102, K.105, E.142, Y.144 Ligands: MG.5, MG.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.68, B:Y.101, B:Y.101 Hydrogen bonds: B:R.72, B:R.72, B:Y.101, B:Y.101 Salt bridges: B:K.17, B:R.41, B:R.93 pi-Stacking: B:F.68 Halogen bonds: B:N.65 BVP.9: 7 residues within 4Å: Chain A: N.60, H.62, I.63 Chain B: L.66, A.70, W.73, S.117 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:H.62, B:W.73 Hydrogen bonds: A:N.60, B:S.117 Salt bridges: A:H.62 pi-Stacking: B:W.73, B:W.73

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain A: K.14, S.15, G.16, K.17, T.18 Ligands: MG.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.14, A:S.15, A:S.15, A:G.16, A:K.17, A:T.18, A:T.18 Salt bridges: A:K.17 SO4.8: 7 residues within 4Å: Chain B: D.13, K.14, S.15, G.16, K.17, T.18 Ligands: MG.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.14, B:S.15, B:G.16, B:K.17, B:T.18, B:T.18 Salt bridges: 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

Related Entries With Identical Sequence