SMTL ID : 1e9e.1

Mutant human thymidylate kinase (F105Y) complexed with dTMP and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.1: 14 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, Y.108, E.152, Y.154 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.45 Hydrogen bonds: A:R.48, A:R.79, A:R.79 Water bridges: A:K.22, A:S.23, A:S.23, A:D.99, A:D.99, A:R.100, A:R.100, A:G.105, A:T.109, A:R.153, A:Y.154, A:E.155, A:Q.160 Salt bridges: A:R.100 pi-Stacking: A:F.75 TMP.5: 14 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, Y.108, E.152, Y.154 Ligands: MG.7 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.45 Hydrogen bonds: B:R.48, B:R.79, B:R.79 Water bridges: B:K.22, B:S.23, B:S.23, B:D.99, B:D.99, B:R.100, B:R.100, B:G.105, B:T.109, B:T.109, B:T.109, B:R.153, B:E.155, B:Q.160 Salt bridges: B:R.100 pi-Stacking: B:F.75

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

ADP.2: 12 residues within 4Å: Chain A: V.17, R.19, A.20, G.21, K.22, S.23, T.24, R.146, K.185, S.186, I.187 Ligands: MG.3 19 PLIP interactions: 19 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:R.146, A:K.185 Water bridges: A:K.22, A:S.23, A:S.23, A:R.27, A:R.100, A:R.146, A:R.146, A:I.187 Salt bridges: A:K.22 pi-Cation interactions: A:R.146 ADP.6: 12 residues within 4Å: Chain B: V.17, R.19, A.20, G.21, K.22, S.23, T.24, R.146, K.185, S.186, I.187 Ligands: MG.7 19 PLIP interactions: 19 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:R.146, B:K.185 Water bridges: B:K.22, B:S.23, B:S.23, B:R.27, B:R.100, B:R.146, B:R.146, B:I.187 Salt bridges: B:K.22 pi-Cation interactions: B:R.146

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

MG.3: 3 residues within 4Å: Chain A: S.23 Ligands: TMP.1, ADP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.23, H2O.2, H2O.6, H2O.12, H2O.12 MG.4: 1 residues within 4Å: Ligands: MG.8 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: S.23 Ligands: TMP.5, ADP.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.23, H2O.14, H2O.18, H2O.24, H2O.24 MG.8: 1 residues within 4Å: Ligands: MG.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ostermann, N. et al., Potentiating Azt Activation: Structures of Wildtype and Mutant Human Thymidylate Kinase Suggest Reasons for the Mutants' Improved Kinetics with the HIV Prodrug Metabolite Aztmp. J.Mol.Biol. (2000)

Release Date

2001-10-11

Peptides

THYMIDYLATE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

THYMIDYLATE KINASE

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