SMTL ID : 4oqm.1

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with F-ARA-EdU

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x FDU: 1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione(Non-covalent)

FDU.1: 15 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.123, A.124, Y.128, R.178, E.181 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.88, A:A.123, A:A.124 Hydrogen bonds: A:E.39, A:Q.81, A:Q.81, A:E.181 Water bridges: A:K.18, A:R.132, A:R.132 pi-Stacking: A:Y.128 FDU.6: 14 residues within 4Å: Chain B: H.14, E.39, W.44, I.53, I.56, Y.57, Q.81, M.84, Y.88, R.119, A.123, A.124, Y.128, E.181 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.44, B:Y.88, B:A.123, B:A.124 Hydrogen bonds: B:E.39, B:Y.57, B:Q.81, B:Q.81, B:R.119, B:E.181 Water bridges: B:R.132, B:R.132 pi-Stacking: B:Y.128 Halogen bonds: B:R.119

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

SO4.2: 8 residues within 4Å: Chain A: H.14, G.15, M.16, G.17, K.18, T.19, R.176, R.178 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.15, A:M.16, A:G.17, A:K.18, A:T.19, A:T.19 Salt bridges: A:K.18, A:R.176, A:R.178 SO4.3: 4 residues within 4Å: Chain A: R.168, D.171, R.172, K.175 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.168, A:R.172, A:K.175 SO4.4: 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 SO4.5: 1 residues within 4Å: Chain A: R.45 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.45 SO4.7: 7 residues within 4Å: Chain B: P.13, H.14, G.15, M.16, G.17, K.18, T.19 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:P.13, B:G.15, B:M.16, B:G.17, B:K.18, B:T.19, B:R.172 Water bridges: B:K.18, B:K.18, B:T.19, B:T.19, B:T.20, B:R.119 Salt bridges: B:K.18 SO4.8: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pernot, L. et al., Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with F-ARA-EdU. To be Published

Release Date

2014-08-13

Peptides

Thymidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidine kinase

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