SMTL ID : 3f0t.1

Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with N-methyl-DHBT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: H.14, G.15, M.16, G.17, R.176, R.178 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.15, A:G.17 Water bridges: A:P.13, A:M.16, A:M.16, A:T.22, A:R.119, A:R.178, A:Y.285 Salt bridges: A:R.176, A:R.178 SO4.2: 2 residues within 4Å: Chain A: H.61, R.182 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.61, A:R.182 SO4.3: 2 residues within 4Å: Chain A: R.168, R.172 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.168, A:R.172, A:K.175 SO4.5: 7 residues within 4Å: Chain B: H.14, G.15, M.16, G.17, K.18, T.19, R.172 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.15, B:M.16, B:G.17, B:K.18, B:T.19, B:T.19, B:R.172 Water bridges: B:G.17, B:K.18, B:K.18, B:K.18, B:K.18, B:R.172 Salt bridges: B:K.18 SO4.6: 3 residues within 4Å: Chain B: K.273, R.276, S.277 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.277, B:S.277 Salt bridges: B:K.273, B:R.276 SO4.7: 3 residues within 4Å: Chain B: R.168, R.172, R.176 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.168, B:K.175, B:R.176

2 x NCV: N-Methyl-6-(1,3-dihydroxy-isobutyl)thymine(Non-covalent)

NCV.4: 13 residues within 4Å: Chain A: H.14, E.39, W.44, I.53, I.56, Y.57, Q.81, M.84, Y.88, R.119, A.124, Y.128, R.178 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.128, A:Y.128 Hydrogen bonds: A:Q.81, A:Q.81, A:R.119, A:R.119 Water bridges: A:E.39, A:R.132, A:R.132, A:R.178 pi-Stacking: A:Y.128 NCV.8: 11 residues within 4Å: Chain B: H.14, E.39, W.44, I.56, Y.57, Q.81, M.84, R.119, A.124, Y.128, R.132 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.128, B:Y.128 Hydrogen bonds: B:Q.81, B:Q.81, B:R.119, B:R.132 Water bridges: B:E.39, B:R.119, B:E.181, B:E.181 pi-Stacking: B:Y.128

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

2009-11-03

Peptides

Thymidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidine kinase

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