SMTL ID : 1e99.1

Human thymidylate kinase complexed with AZTMP and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

ATM.1: 16 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, E.152, R.153, Y.154, E.155, Q.160 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.45, A:F.108 Hydrogen bonds: A:R.48, A:R.79, A:R.79, A:Y.154, A:Q.160 Water bridges: A:K.22, A:S.23, A:S.23, A:S.76, A:D.99, A:D.99, A:R.100, A:R.100, 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 ATM.5: 16 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, E.152, R.153, Y.154, E.155, Q.160 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:F.45, B:F.108 Hydrogen bonds: B:R.48, B:R.79, B:R.79, B:Q.160 Water bridges: B:D.18, B:K.22, B:S.23, B:S.23, B:S.76, B:D.99, B:D.99, B:R.100, B:R.100, B:R.100, B:R.100, B:G.105, B:T.109, B:T.109, B:T.109, B:E.155 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: R.19, A.20, G.21, K.22, S.23, T.24, R.146, A.183, K.185, S.186, I.187 Ligands: MG.3 16 PLIP interactions: 16 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:V.17, A:K.22, A:S.23, A:S.23, A:Q.25 Salt bridges: A:K.22 pi-Cation interactions: A:R.146 ADP.6: 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.7 16 PLIP interactions: 16 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:V.17, B:K.22, B:S.23, B:S.23, B:Q.25 Salt bridges: B:K.22 pi-Cation interactions: B:R.146

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

MG.3: 2 residues within 4Å: Chain A: S.23 Ligands: ADP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.23, H2O.2, H2O.6, H2O.11, H2O.11 MG.4: 1 residues within 4Å: Ligands: MG.8 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: S.23 Ligands: ADP.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.23, H2O.13, H2O.17, H2O.22, H2O.22 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

2001-10-05

Peptides

THYMIDYLATE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

THYMIDYLATE KINASE

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