SMTL ID : 1e9a.1

Human thymidylate kinase complexed with the bisubstrate inhibitor AZTP5A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x Z5A: P1-(5'-ADENOSYL)P5-(5'-(3'AZIDO-3'-DEOXYTHYMIDYL))PENTAPHOSPHATE(Non-covalent)

Z5A.1: 25 residues within 4Å: Chain A: D.18, R.19, A.20, G.21, K.22, S.23, T.24, F.45, P.46, R.48, L.60, F.75, R.79, R.100, S.104, G.105, F.108, R.146, Y.154, Q.160, A.183, K.185, S.186, I.187 Ligands: MG.2 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:F.45, A:F.108 Hydrogen bonds: A:D.18, A:R.19, A:A.20, A:G.21, A:K.22, A:S.23, A:T.24, A:T.24, A:R.48, A:R.79, A:R.79, A:R.146, A:R.146, A:Q.160, A:K.185 Water bridges: A:S.23, A:S.23, A:S.23, A:R.27, A:F.45, A:R.48, A:G.105, A:T.109, A:Y.154 Salt bridges: A:K.22, A:K.22, A:R.100, A:R.100 pi-Stacking: A:F.75 pi-Cation interactions: A:R.146 Z5A.4: 25 residues within 4Å: Chain B: D.18, R.19, A.20, G.21, K.22, S.23, T.24, F.45, P.46, R.48, L.60, F.75, R.79, R.100, S.104, G.105, F.108, R.146, Y.154, Q.160, A.183, K.185, S.186, I.187 Ligands: MG.5 37 PLIP interactions: 37 interactions with chain B Hydrophobic interactions: B:F.45, B:F.108 Hydrogen bonds: B:D.18, B:R.19, B:A.20, B:G.21, B:K.22, B:S.23, B:T.24, B:T.24, B:R.48, B:R.79, B:R.79, B:R.146, B:R.146, B:Y.154, B:Q.160, B:K.185 Water bridges: B:S.23, B:S.23, B:S.23, B:R.27, B:F.45, B:R.48, B:G.105, B:T.109, B:T.109, B:T.109, B:E.155, B:E.155, B:E.155 Salt bridges: B:K.22, B:K.22, B:R.100, B:R.100 pi-Stacking: B:F.75 pi-Cation interactions: B:R.146

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

MG.2: 2 residues within 4Å: Chain A: S.23 Ligands: Z5A.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.23, H2O.2, H2O.6, H2O.11 MG.3: 1 residues within 4Å: Ligands: MG.6 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: S.23 Ligands: Z5A.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.23, H2O.13, H2O.17, H2O.22 MG.6: 1 residues within 4Å: Ligands: MG.3 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

2001-10-05

Peptides

THYMIDYLATE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

THYMIDYLATE KINASE

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