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

Crystal structure of EHV4-TK complexed with TP5A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.02 Å

Oligo State

homo-octamer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.109, L.312 Chain E: Q.184 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: R.154, P.156, Q.157 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: R.240, V.241, S.242 Chain E: Q.238 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: R.214, G.216, W.217, G.218, E.219 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: F.51, E.52, T.53, R.86 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain B: R.109, L.312 Chain G: Q.184 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: R.154, P.156, Q.157 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: R.240, V.241, S.242 Chain G: Q.238 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain B: R.214, G.216, W.217, G.218, E.219 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: F.51, E.52, T.53, R.86 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: 3 residues within 4Å: Chain C: R.240, V.241, S.242 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain D: F.51, E.52, T.53, R.86 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain D: R.240, V.241, S.242 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain E: R.154, P.156, Q.157 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain E: F.51, E.52, T.53, R.86 Ligand excluded by PLIP SO4.21: 7 residues within 4Å: Chain B: H.229, Q.233 Chain E: S.106, Q.157, G.158, R.208, S.309 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain E: T.293, R.295, Q.296 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain E: R.295, Q.296 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain E: G.216, W.217, G.218, E.219 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain E: R.240, V.241, S.242 Ligand excluded by PLIP SO4.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain F: F.51, E.52, T.53, R.86 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain G: R.154, P.156, Q.157 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain G: F.51, E.52, T.53, R.86 Ligand excluded by PLIP SO4.32: 7 residues within 4Å: Chain A: H.229, Q.233 Chain G: S.106, Q.157, G.158, R.208, S.309 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain G: T.293, R.295, Q.296 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain G: R.295, Q.296 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain G: G.216, W.217, G.218, E.219 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain G: R.240, V.241, S.242 Ligand excluded by PLIP SO4.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain H: F.51, E.52, T.53, R.86 Ligand excluded by PLIP

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

T5A.6: 23 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, I.56, Y.60, Q.84, F.87, R.121, S.126, F.130, R.134, R.174, G.292, T.293, P.294 Ligands: T5A.15 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.16, 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:Q.84, A:Q.84, A:R.121, A:R.134, A:R.174, A:G.292 Salt bridges: A:K.20, A:K.20, A:K.20 pi-Stacking: A:F.87, A:F.130 pi-Cation interactions: A:R.174 T5A.12: 23 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, I.56, Y.60, Q.84, F.87, R.121, S.126, F.130, R.134, R.174, G.292, T.293, P.294 Ligands: T5A.18 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.16, B:F.130 Hydrogen bonds: 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:Q.84, B:Q.84, B:R.121, B:R.134, B:R.174, B:G.292 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 T5A.15: 24 residues within 4Å: Chain A: T.177 Chain C: 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 Ligands: T5A.6 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:Y.16, C:F.87, C:F.130 Hydrogen bonds: C:G.17, C:G.17, C:I.18, C:G.19, C:K.20, C:S.21, C:S.21, C:T.22, C:T.22, C:E.42, C:E.42, C:Y.60, C:Q.84, C:Q.84, C:R.121, C:R.134, C:R.174, C:R.174, C:G.292 Salt bridges: C:K.20, C:K.20, C:K.20 pi-Stacking: C:F.87, C:F.130 pi-Cation interactions: C:R.174 T5A.18: 24 residues within 4Å: Chain B: T.177 Chain D: 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 Ligands: T5A.12 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:Y.16, D:F.87, D:F.130 Hydrogen bonds: D:G.17, D:G.17, D:I.18, D:G.19, D:K.20, D:S.21, D:S.21, D:T.22, D:T.22, D:E.42, D:E.42, D:Y.60, D:Q.84, D:Q.84, D:R.121, D:R.134, D:R.174, D:R.174, D:G.292 Salt bridges: D:K.20, D:K.20, D:K.20 pi-Stacking: D:F.87, D:F.130 pi-Cation interactions: D:R.174 T5A.26: 22 residues within 4Å: Chain E: Y.16, G.17, I.18, G.19, K.20, S.21, T.22, E.42, M.44, W.47, Q.84, F.87, Y.91, R.121, S.126, F.130, R.174, R.178, G.292, T.293, P.294, C.297 22 PLIP interactions: 22 interactions with chain E Hydrophobic interactions: E:F.130 Hydrogen bonds: E:G.17, E:I.18, E:G.19, E:K.20, E:S.21, E:S.21, E:T.22, E:T.22, E:E.42, E:E.42, E:E.42, E:Q.84, E:Q.84, E:R.121, E:G.292 Salt bridges: E:K.20, E:K.20, E:R.178 pi-Stacking: E:F.87, E:F.130 pi-Cation interactions: E:R.174 T5A.29: 22 residues within 4Å: Chain F: 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 F Hydrophobic interactions: F:W.47, F:F.130 Hydrogen bonds: F:G.17, F:I.18, F:G.19, F:K.20, F:S.21, F:S.21, F:T.22, F:T.22, F:E.42, F:E.42, F:Y.60, F:Q.84, F:Q.84, F:G.292 Water bridges: F:R.134, F:R.134 Salt bridges: F:K.20, F:K.20 pi-Stacking: F:F.87, F:F.130 pi-Cation interactions: F:R.174 T5A.37: 22 residues within 4Å: Chain G: Y.16, G.17, I.18, G.19, K.20, S.21, T.22, E.42, M.44, W.47, Q.84, F.87, Y.91, R.121, S.126, F.130, R.174, R.178, G.292, T.293, P.294, C.297 22 PLIP interactions: 22 interactions with chain G Hydrophobic interactions: G:F.130 Hydrogen bonds: G:G.17, G:I.18, G:G.19, G:K.20, G:S.21, G:S.21, G:T.22, G:T.22, G:E.42, G:E.42, G:E.42, G:Q.84, G:Q.84, G:R.121, G:G.292 Salt bridges: G:K.20, G:K.20, G:R.178 pi-Stacking: G:F.87, G:F.130 pi-Cation interactions: G:R.174 T5A.40: 22 residues within 4Å: Chain H: 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 H Hydrophobic interactions: H:W.47, H:F.130 Hydrogen bonds: H:G.17, H:I.18, H:G.19, H:K.20, H:S.21, H:S.21, H:T.22, H:T.22, H:E.42, H:E.42, H:Y.60, H:Q.84, H:Q.84, H:G.292 Water bridges: H:R.134, H:R.134 Salt bridges: H:K.20, H:K.20 pi-Stacking: H:F.87, H:F.130 pi-Cation interactions: H: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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
D

D
D

E
B

F
C

G
B

H
C

Thymidine kinase

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