SMTL ID : 1p72.1 (3 other biounits)

Crystal structure of EHV4-TK complexed with Thy and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: F.51, E.52, T.53, R.86 Chain B: S.141, C.143 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.52, A:T.53, A:T.53, B:S.141, B:S.141 Water bridges: A:R.86, A:R.86, A:R.86 Salt bridges: A:R.86 SO4.2: 4 residues within 4Å: Chain A: R.154, P.156, Q.157, N.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.157, A:Q.157, A:N.282 Salt bridges: A:R.154 SO4.3: 1 residues within 4Å: Chain A: Q.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.184 SO4.4: 2 residues within 4Å: Chain A: R.295, Q.296 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.296 Salt bridges: A:R.295 SO4.5: 2 residues within 4Å: Chain A: R.154 Chain B: R.154 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.154 Salt bridges: B:R.154, A:R.154 SO4.8: 6 residues within 4Å: Chain A: S.141, C.143 Chain B: F.51, E.52, T.53, R.86 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.52, B:T.53, B:T.53, A:S.141, A:S.141 Water bridges: B:R.86, B:R.86, B:R.86 Salt bridges: B:R.86 SO4.9: 4 residues within 4Å: Chain B: R.154, P.156, Q.157, N.282 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.157, B:Q.157, B:N.282 Salt bridges: B:R.154 SO4.10: 1 residues within 4Å: Chain B: T.293 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.293 Water bridges: B:Q.296 SO4.11: 1 residues within 4Å: Chain B: R.176 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.176 Salt bridges: B:R.176

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.6: 14 residues within 4Å: Chain A: V.15, Y.16, G.17, I.18, G.19, K.20, S.21, T.22, R.174, R.178, G.292, T.293, P.294, C.297 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:V.15, A:G.17, A:I.18, A:G.19, A:K.20, A:S.21, A:T.22, A:T.22, A:R.174, A:G.292 Water bridges: A:K.20, A:S.21, A:T.22, A:E.42, A:R.173, A:R.178, A:R.178, A:R.178 Salt bridges: A:K.20, A:R.178 pi-Cation interactions: A:R.174 ADP.12: 15 residues within 4Å: Chain B: V.15, Y.16, G.17, I.18, G.19, K.20, S.21, T.22, R.174, T.177, R.178, G.292, T.293, P.294, C.297 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:V.15, B:G.17, B:I.18, B:G.19, B:K.20, B:S.21, B:T.22, B:T.22, B:T.177, B:T.177, B:G.292 Water bridges: B:K.20, B:R.25, B:R.25, B:E.42, B:R.178, B:R.178, B:R.178 Salt bridges: B:K.20, B:R.178 pi-Cation interactions: B:R.174

2 x THM: THYMIDINE(Non-covalent)

THM.7: 10 residues within 4Å: Chain A: Y.16, E.42, W.47, I.56, Y.60, Q.84, F.87, R.121, S.126, F.130 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.16, A:W.47, A:F.130 Hydrogen bonds: A:E.42, A:Q.84, A:Q.84, A:R.121 Water bridges: A:R.134, A:R.134 pi-Stacking: A:F.87, A:F.130 THM.13: 10 residues within 4Å: Chain B: Y.16, E.42, W.47, I.56, Q.84, F.87, R.121, S.126, F.130, E.183 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.16, B:W.47, B:F.130 Hydrogen bonds: B:E.42, B:Q.84, B:Q.84, B:R.121, B:E.183 Water bridges: B:R.134, B:R.178, B:Q.184 pi-Stacking: B:F.87, B:F.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gardberg, A. et al., Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases. Structure (2003)

Release Date

2003-11-04

Peptides

Thymidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidine kinase

Related Entries With Identical Sequence