SMTL ID : 1e9b.1

Human thymidylate kinase complexed with AZTMP and APPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

ATM.1: 15 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, E.155, Q.160 Ligands: ANP.3 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:F.45, A:F.108 Hydrogen bonds: A:R.79, A:R.79, A:Y.154, A:Q.160 Water bridges: A:S.23, A:R.48, A:R.48, A:R.48, A:R.48, A:D.99, A:D.99, A:D.99, A:D.99, A:D.99, A:D.99, A:R.100, A:R.100, A:R.100, A:R.100, A:G.105, A:T.109, A:E.152, A:Y.154 Salt bridges: A:R.48, A:R.100 pi-Stacking: A:F.75 ATM.6: 15 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, E.155, Q.160 Ligands: ANP.8 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:F.45, B:F.108 Hydrogen bonds: B:R.79, B:R.79, B:Y.154, B:Q.160 Water bridges: B:S.23, B:R.48, B:R.48, B:R.48, B:R.48, B:R.48, B:D.99, B:D.99, B:D.99, B:D.99, 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.48, B:R.100 pi-Stacking: B:F.75

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

ADP.2: 14 residues within 4Å: Chain A: V.17, R.19, A.20, G.21, K.22, S.23, T.24, R.146, A.183, K.185, S.186, I.187 Ligands: ANP.3, MG.4 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:K.185 Water bridges: A:K.22, A:K.22, A:S.23, A:S.23, A:S.23, A:D.99, A:R.146, A:R.146, A:I.187 Salt bridges: A:K.22 pi-Cation interactions: A:R.146 ADP.7: 14 residues within 4Å: Chain B: V.17, R.19, A.20, G.21, K.22, S.23, T.24, R.146, A.183, K.185, S.186, I.187 Ligands: ANP.8, MG.9 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:K.185 Water bridges: B:K.22, B:K.22, B:S.23, B:S.23, B:S.23, B:D.99, B:R.146, B:R.146, B:I.187 Salt bridges: B:K.22 pi-Cation interactions: B:R.146

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 16 residues within 4Å: Chain A: D.18, R.19, A.20, G.21, K.22, S.23, T.24, R.100, R.146, A.183, K.185, S.186, I.187 Ligands: ATM.1, ADP.2, MG.4 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.19, A:A.20, A:G.21, A:K.22, A:K.22, A:S.23, A:T.24, A:T.24, A:R.100, A:K.185 Water bridges: A:D.18, A:S.23, A:S.23, A:S.23, A:S.23, A:Q.25, A:R.146, A:R.146, A:I.187 pi-Cation interactions: A:R.146 ANP.8: 16 residues within 4Å: Chain B: D.18, R.19, A.20, G.21, K.22, S.23, T.24, R.100, R.146, A.183, K.185, S.186, I.187 Ligands: ATM.6, ADP.7, MG.9 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:D.18, B:R.19, B:A.20, B:G.21, B:K.22, B:K.22, B:S.23, B:T.24, B:T.24, B:R.100, B:K.185 Water bridges: B:D.18, B:S.23, B:S.23, B:S.23, B:S.23, B:Q.25, B:R.146, B:R.146, B:I.187 pi-Cation interactions: B:R.146

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

MG.4: 3 residues within 4Å: Chain A: S.23 Ligands: ADP.2, ANP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.23, H2O.2, H2O.6, H2O.11, H2O.12 MG.5: 1 residues within 4Å: Ligands: MG.10 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: S.23 Ligands: ADP.7, ANP.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.23, H2O.13, H2O.18, H2O.23, H2O.23 MG.10: 1 residues within 4Å: Ligands: MG.5 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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