SMTL ID : 1p72.2 (3 other biounits)

Crystal structure of EHV4-TK complexed with Thy and ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: F.51, E.52, T.53, R.86 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: R.154, P.156, Q.157, N.282 Ligand excluded by PLIP SO4.3: 1 residues within 4Å: Chain A: T.293 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.176 Chain D: T.111, Q.112 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain B: F.51, E.52, T.53, R.86 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: R.154, P.156, Q.157, N.282 Ligand excluded by PLIP SO4.9: 1 residues within 4Å: Chain B: T.293 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: R.176 Chain C: T.111, Q.112 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain C: F.51, E.52, T.53, R.86 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain C: R.154, P.156, Q.157, N.282 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: L.107, R.109 Chain C: Q.184 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain C: R.295, Q.296 Ligand excluded by PLIP SO4.17: 1 residues within 4Å: Chain C: R.154 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain D: F.51, E.52, T.53, R.86 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain D: R.154, P.156, Q.157, N.282 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: L.107, R.109 Chain D: Q.184 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain D: R.295, Q.296 Ligand excluded by PLIP SO4.24: 1 residues within 4Å: Chain D: R.154 Ligand excluded by PLIP

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

ADP.5: 15 residues within 4Å: Chain A: 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 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:T.177, A:T.177, A:G.292 Water bridges: A:K.20, A:R.25, A:R.25, A:E.42, A:R.178, A:R.178, A:R.178 Salt bridges: A:K.20, A:R.178 pi-Cation interactions: A:R.174 ADP.11: 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 20 PLIP interactions: 20 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: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 ADP.18: 14 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:V.15, C:G.17, C:I.18, C:G.19, C:K.20, C:S.21, C:T.22, C:T.22, C:R.174, C:G.292 Water bridges: C:K.20, C:S.21, C:T.22, C:E.42, C:R.173, C:R.178, C:R.178, C:R.178 Salt bridges: C:K.20, C:R.178 pi-Cation interactions: C:R.174 ADP.25: 14 residues within 4Å: Chain D: 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 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:V.15, D:G.17, D:I.18, D:G.19, D:K.20, D:S.21, D:T.22, D:T.22, D:R.174, D:G.292 Water bridges: D:K.20, D:S.21, D:T.22, D:T.23, D:E.42, D:R.173, D:R.178, D:R.178, D:R.178 Salt bridges: D:K.20, D:R.178 pi-Cation interactions: D:R.174

4 x THM: THYMIDINE(Non-covalent)

THM.6: 10 residues within 4Å: Chain A: 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 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, A:E.183 Water bridges: A:R.134, A:R.178, A:Q.184 pi-Stacking: A:F.87, A:F.130 THM.12: 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 14 PLIP interactions: 14 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, B:E.183 Water bridges: B:R.134, B:R.178, B:Q.184 pi-Stacking: B:F.87, B:F.130 THM.19: 10 residues within 4Å: Chain C: 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 C Hydrophobic interactions: C:Y.16, C:W.47, C:F.130 Hydrogen bonds: C:E.42, C:Q.84, C:Q.84, C:R.121 Water bridges: C:R.134, C:R.134 pi-Stacking: C:F.87, C:F.130 THM.26: 10 residues within 4Å: Chain D: Y.16, E.42, W.47, I.56, Y.60, Q.84, F.87, R.121, S.126, F.130 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.16, D:W.47, D:F.130 Hydrogen bonds: D:E.42, D:Y.60, D:Q.84, D:Q.84, D:R.121 Water bridges: D:R.134, D:R.134 pi-Stacking: D:F.87, D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
A

D
A

Thymidine kinase

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