SMTL ID : 2j87.1

Structure of vaccinia virus thymidine kinase in complex with dTTP: insights for drug design

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-tetramer

Ligands

4 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 23 residues within 4Å: Chain A: P.12, M.13, F.14, S.15, G.16, K.17, S.18, D.82, E.83, F.86, L.109, T.112, F.113, F.118, S.148, R.150, I.157, E.158, I.159, I.160, G.161, Y.166 Ligands: MG.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.166, A:Y.166 Hydrogen bonds: A:P.12, A:F.14, A:S.15, A:G.16, A:K.17, A:S.18, A:S.18, A:D.82, A:E.83, A:E.83, A:F.113, A:R.150, A:I.157, A:I.159 Salt bridges: A:K.17, A:K.17, A:K.17 pi-Stacking: A:F.118 TTP.4: 25 residues within 4Å: Chain B: P.12, M.13, F.14, S.15, G.16, K.17, S.18, T.19, N.42, D.82, E.83, F.86, L.109, T.112, F.113, F.118, S.148, R.150, I.157, E.158, I.159, I.160, G.161, Y.166 Ligands: MG.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.166, B:Y.166 Hydrogen bonds: B:F.14, B:S.15, B:G.16, B:K.17, B:S.18, B:S.18, B:T.19, B:E.83, B:F.113, B:R.150, B:I.157, B:I.159, B:Y.166 Salt bridges: B:K.17, B:K.17, B:K.17 TTP.7: 22 residues within 4Å: Chain C: P.12, M.13, F.14, S.15, G.16, K.17, S.18, D.82, E.83, F.86, L.109, T.112, F.113, F.118, R.150, I.157, E.158, I.159, I.160, G.161, Y.166 Ligands: MG.9 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:Y.166, C:Y.166 Hydrogen bonds: C:F.14, C:S.15, C:G.16, C:K.17, C:S.18, C:S.18, C:D.82, C:E.83, C:E.83, C:F.113, C:R.150, C:I.157, C:I.159, C:Y.166 Salt bridges: C:K.17, C:K.17, C:K.17 pi-Stacking: C:F.118 TTP.10: 23 residues within 4Å: Chain D: P.12, M.13, F.14, S.15, G.16, K.17, S.18, D.82, E.83, F.86, L.109, T.112, F.113, F.118, S.148, R.150, I.157, E.158, I.159, I.160, G.161, Y.166 Ligands: MG.12 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:Y.166 Hydrogen bonds: D:P.12, D:F.14, D:S.15, D:G.16, D:K.17, D:S.18, D:S.18, D:S.18, D:E.83, D:F.113, D:R.150, D:I.157, D:I.159, D:Y.166 Salt bridges: D:K.17, D:K.17, D:K.17 pi-Stacking: D:F.118, D:Y.166

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.138, C.141, C.170, C.173 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.138, A:C.141, A:C.170, A:C.173 ZN.5: 5 residues within 4Å: Chain B: C.138, K.140, C.141, C.170, C.173 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.138, B:C.141, B:C.170, B:C.173 ZN.8: 4 residues within 4Å: Chain C: C.138, C.141, C.170, C.173 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.138, C:C.141, C:C.170, C:C.173 ZN.11: 4 residues within 4Å: Chain D: C.138, C.141, C.170, C.173 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.138, D:C.141, D:C.170, D:C.173

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: M.13, F.14 Ligands: TTP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: M.13, F.14 Ligands: TTP.4 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain C: M.13 Ligands: TTP.7 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain D: M.13, F.14 Ligands: TTP.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

El Omari, K. et al., Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights for Drug Design. Bmc Struct.Biol. (2006)

Release Date

2006-11-13

Peptides

THYMIDINE KINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

THYMIDINE KINASE