SMTL ID : 1p75.2 (3 other biounits)

Crystal structure of EHV4-TK complexed with TP5A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.02 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.2: 7 residues within 4Å: Chain A: F.51, E.52, T.53, R.86 Chain B: S.141, C.143, E.257 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.141, A:E.52, A:T.53, A:T.53 Water bridges: A:R.86 Salt bridges: A:R.86 SO4.4: 6 residues within 4Å: Chain A: S.141, C.143 Chain B: F.51, E.52, T.53, R.86 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.52, B:T.53, A:S.141, A:S.141 Water bridges: B:R.86, B:R.86 Salt bridges: B:R.86 SO4.5: 3 residues within 4Å: Chain B: R.240, V.241, S.242 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.241, B:S.242 Salt bridges: B:R.240

2 x T5A: P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE(Non-covalent)

T5A.3: 22 residues within 4Å: Chain A: Y.16, G.17, I.18, G.19, K.20, S.21, T.22, E.42, M.44, W.47, Y.60, Q.84, F.87, R.121, S.126, F.130, R.174, T.177, R.178, G.292, T.293, P.294 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:W.47, A:F.130 Hydrogen bonds: A:G.17, A:I.18, A:G.19, A:K.20, A:S.21, A:S.21, A:T.22, A:T.22, A:E.42, A:E.42, A:Y.60, A:Q.84, A:Q.84, A:G.292 Water bridges: A:R.134, A:R.134 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:F.87, A:F.130 pi-Cation interactions: A:R.174 T5A.6: 22 residues within 4Å: Chain B: Y.16, G.17, I.18, G.19, K.20, S.21, T.22, E.42, M.44, W.47, Y.60, Q.84, F.87, R.121, S.126, F.130, R.134, R.174, G.292, T.293, P.294, C.297 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:Y.16, B:F.87, B:F.130 Hydrogen bonds: B:G.17, B:G.17, B:I.18, B:G.19, B:K.20, B:S.21, B:S.21, B:T.22, B:T.22, B:E.42, B:E.42, B:Q.84, B:Q.84, B:R.121, B:R.134, B:R.174, B:R.174, B:G.292 Water bridges: B:Y.16 Salt bridges: B:K.20, B:K.20, B:K.20 pi-Stacking: B:F.87, B:F.130 pi-Cation interactions: B:R.174

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
C

B
D

Thymidine kinase

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