SMTL ID : 1nn0.1

Crystal structure of human thymidylate kinase with ddTMP and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: S.23 Ligands: ADP.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.23, H2O.1, H2O.1, H2O.1, H2O.8 MG.2: 1 residues within 4Å: Ligands: MG.6 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: S.23 Ligands: ADP.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.23, H2O.12, H2O.12, H2O.12, H2O.20 MG.6: 1 residues within 4Å: Ligands: MG.2 No protein-ligand interaction detected (PLIP)

2 x 2DT: 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE(Non-covalent)

2DT.3: 12 residues within 4Å: Chain A: F.45, P.46, R.48, L.60, F.75, R.79, R.100, Y.101, S.104, G.105, F.108, Y.154 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.45, A:F.108 Hydrogen bonds: A:R.48, A:R.79, A:R.79 Water bridges: A:K.22, A:K.22, A:S.23, A:R.100, A:R.100, A:R.100, A:G.105, A:T.109, A:Y.154 Salt bridges: A:R.100 pi-Stacking: A:F.75 2DT.7: 12 residues within 4Å: Chain B: F.45, P.46, R.48, L.60, F.75, R.79, R.100, Y.101, S.104, G.105, F.108, Y.154 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.45, B:F.108 Hydrogen bonds: B:R.48, B:R.79, B:R.79 Water bridges: B:K.22, B:K.22, B:S.23, B:R.100, B:R.100, B:R.100, B:G.105, B:T.109, B:T.109, B:T.109 Salt bridges: B:R.100 pi-Stacking: B:F.75

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

ADP.4: 12 residues within 4Å: Chain A: R.19, A.20, G.21, K.22, S.23, T.24, R.146, A.183, K.185, S.186, I.187 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.19, A:A.20, A:G.21, A:K.22, A:S.23, A:T.24, A:T.24, A:K.185 Water bridges: A:D.18, A:K.22, A:K.22, A:S.23, A:S.23, A:Q.25, A:R.27, A:R.146, A:R.146, A:I.187 Salt bridges: A:K.22 pi-Cation interactions: A:R.146 ADP.8: 12 residues within 4Å: Chain B: R.19, A.20, G.21, K.22, S.23, T.24, R.146, A.183, K.185, S.186, I.187 Ligands: MG.5 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:R.19, B:A.20, B:G.21, B:K.22, B:S.23, B:T.24, B:T.24, B:K.185 Water bridges: B:D.18, B:K.22, B:K.22, B:S.23, B:S.23, B:Q.25, B:R.27, B:R.146, B:R.146, B:I.187 Salt bridges: B:K.22 pi-Cation interactions: B:R.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ostermann, N. et al., Structures of human thymidylate kinase in complex with prodrugs: implications for the structure-based design of novel compounds. Biochemistry (2003)

Release Date

2003-03-18

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thymidylate kinase

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