SMTL ID : 1e2i.1

The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: H.13, G.14, M.15, G.16, K.17, T.18, R.175, R.177 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.14, A:G.16, A:K.17, A:T.18, A:R.175 Water bridges: A:R.118, A:R.118, A:R.177 Salt bridges: A:K.17, A:R.177 SO4.4: 7 residues within 4Å: Chain B: H.13, G.14, M.15, G.16, K.17, T.18, R.171 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.14, B:M.15, B:G.16, B:K.17, B:T.18, B:R.171 Water bridges: B:G.16, B:K.17, B:K.17, B:T.18, B:R.118 Salt bridges: B:K.17

2 x APS: 9-HYDROXYPROPYLADENINE, S-ISOMER(Non-covalent)

APS.2: 12 residues within 4Å: Chain A: H.13, E.38, W.43, I.52, I.55, Q.80, M.83, R.118, A.123, Y.127, R.177 Ligands: ARP.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.43, A:I.52, A:R.177 Hydrogen bonds: A:Q.80, A:R.118 Water bridges: A:R.118, A:R.131 pi-Stacking: A:Y.127, A:Y.127 APS.5: 10 residues within 4Å: Chain B: H.13, W.43, Q.80, M.83, Y.87, R.118, A.123, Y.127, E.180 Ligands: ARP.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.80, B:Q.80, B:Y.87, B:Y.127, B:Y.127 pi-Stacking: B:Y.127, B:Y.127

2 x ARP: 9-HYDROXYPROPYLADENINE, R-ISOMER(Non-covalent)

ARP.3: 11 residues within 4Å: Chain A: H.13, E.38, I.52, I.55, Q.80, M.83, R.118, A.123, Y.127, R.177 Ligands: APS.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.52, A:R.177 Hydrogen bonds: A:Q.80 Water bridges: A:E.38, A:R.118, A:R.131 pi-Stacking: A:Y.127, A:Y.127 ARP.6: 10 residues within 4Å: Chain B: H.13, W.43, Q.80, M.83, Y.87, R.118, A.123, Y.127, E.180 Ligands: APS.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.127 Hydrogen bonds: B:Q.80, B:Q.80, B:Y.87 pi-Stacking: B:Y.127, B:Y.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vogt, J. et al., Nucleoside Binding Site of Herpes Simplex Type 1 Thymidine Kinase Analyzed by X-Ray Crystallography. Proteins (2000)

Release Date

2000-11-06

Peptides

THYMIDINE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

THYMIDINE KINASE

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