SMTL ID : 1nmz.1

Crystal structure of human thymidylate kinase with NH2TMP and AppNHp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

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

2 x NYM: 3'-DEOXY-3'-AMINOTHYMIDINE MONOPHOSPHATE(Non-covalent)

NYM.3: 14 residues within 4Å: Chain A: D.18, F.45, P.46, R.48, L.60, F.75, R.79, R.100, S.104, G.105, F.108, Y.154 Ligands: MG.1, ANP.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.45, A:F.108 Hydrogen bonds: A:D.18, A:R.48, A:R.79, A:R.79 Water bridges: A:D.18, A:G.105, A:T.109, A:Y.154 Salt bridges: A:R.100 pi-Stacking: A:F.75 NYM.7: 14 residues within 4Å: Chain B: D.18, F.45, P.46, R.48, L.60, F.75, R.79, R.100, S.104, G.105, F.108, Y.154 Ligands: MG.5, ANP.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.45, B:F.108 Hydrogen bonds: B:D.18, B:R.48, B:R.79, B:R.79 Water bridges: B:D.18, 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 ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.4: 15 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: MG.1, NYM.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:D.18, 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:R.146, A:K.185 Water bridges: A:S.23, A:S.23, A:S.23, A:R.27, A:R.146, A:R.146 pi-Cation interactions: A:R.146 ANP.8: 15 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: MG.5, NYM.7 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:D.18, 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:R.146, B:K.185 Water bridges: B:S.23, B:S.23, B:S.23, B:R.27, B:R.146, B:R.146 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

similar to THYMIDYLATE KINASE (DTMP KINASE): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

similar to THYMIDYLATE KINASE (DTMP KINASE)

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