SMTL ID : 3rdp.1

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with N-METHYL-FHBT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: H.13, G.14, M.15, G.16, R.177 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.14, A:M.15, A:G.16, A:T.21 Water bridges: A:R.177 Salt bridges: A:R.177 SO4.3: 7 residues within 4Å: Chain B: H.13, G.14, M.15, G.16, K.17, T.18, R.177 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.14, B:M.15, B:G.16, B:K.17, B:T.18, B:T.18, B:T.18 Water bridges: B:K.17 Salt bridges: B:R.177 SO4.4: 3 residues within 4Å: Chain B: K.272, R.275, S.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.276 Salt bridges: B:K.272, B:R.275

2 x NMF: 6-[(2R)-2-(fluoromethyl)-3-hydroxy-propyl]-1,5-dimethyl-pyrimidine-2,4-dione(Non-covalent)

NMF.2: 12 residues within 4Å: Chain A: H.13, E.38, W.43, I.52, I.55, Y.56, Q.80, M.83, R.118, A.123, Y.127, R.177 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.127, A:Y.127 Hydrogen bonds: A:E.38, A:Q.80, A:Q.80 Water bridges: A:R.131 pi-Stacking: A:Y.127 NMF.5: 11 residues within 4Å: Chain B: E.38, W.43, I.52, I.55, Y.56, Q.80, M.83, R.118, A.123, Y.127, R.177 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.43, B:Y.127, B:Y.127 Hydrogen bonds: B:E.38, B:Q.80, B:Q.80 Water bridges: B:R.131 pi-Stacking: B:Y.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martic, M. et al., Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo. Nucleosides Nucleotides Nucleic Acids (2011)

Release Date

2011-08-03

Peptides

Thymidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidine kinase

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