SMTL ID : 1nmy.2 (1 other biounit)

Crystal structure of human thymidylate kinase with FLTMP and AppNHp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 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.17 Ligands: ADP.4, ANP.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.1, H2O.1, H2O.1 MG.2: 1 residues within 4Å: Ligands: MG.7 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: S.17 Ligands: ADP.9, ANP.10 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.17, H2O.14, H2O.14, H2O.14, H2O.14 MG.7: 1 residues within 4Å: Ligands: MG.2 No protein-ligand interaction detected (PLIP)

2 x FDM: 3'-FLUORO-3'-DEOXYTHYMIDINE MONOPHOSPHATE(Non-covalent)

FDM.3: 15 residues within 4Å: Chain A: F.39, P.40, R.42, L.54, F.69, R.73, R.94, Y.95, S.98, G.99, F.102, E.146, R.147, Y.148 Ligands: ANP.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.39, A:F.102 Hydrogen bonds: A:R.73, A:R.73, A:R.94 Water bridges: A:S.17, A:R.42, A:R.42, A:R.42, A:R.94, A:G.99, A:T.103, A:E.146, A:Y.148 Salt bridges: A:R.42 pi-Stacking: A:F.69 Halogen bonds: A:R.147 FDM.8: 15 residues within 4Å: Chain B: F.39, P.40, R.42, L.54, F.69, R.73, R.94, Y.95, S.98, G.99, F.102, E.146, R.147, Y.148 Ligands: ANP.10 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.39, B:F.102 Hydrogen bonds: B:R.73, B:R.73, B:R.94 Water bridges: B:S.17, B:R.42, B:R.42, B:R.94, B:G.99, B:T.103, B:T.103, B:T.103 Salt bridges: B:R.42 pi-Stacking: B:F.69 Halogen bonds: B:R.147

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

ADP.4: 14 residues within 4Å: Chain A: V.11, R.13, A.14, G.15, K.16, S.17, T.18, R.140, A.177, K.179, S.180, I.181 Ligands: MG.1, ANP.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.13, A:A.14, A:G.15, A:K.16, A:S.17, A:T.18, A:T.18, A:R.140, A:K.179 Water bridges: A:K.16, A:K.16, A:S.17, A:S.17, A:R.21 Salt bridges: A:K.16 pi-Cation interactions: A:R.140 ADP.9: 14 residues within 4Å: Chain B: V.11, R.13, A.14, G.15, K.16, S.17, T.18, R.140, A.177, K.179, S.180, I.181 Ligands: MG.6, ANP.10 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.13, B:A.14, B:G.15, B:K.16, B:S.17, B:T.18, B:T.18, B:R.140, B:K.179 Water bridges: B:K.16, B:K.16, B:S.17, B:S.17, B:R.21 Salt bridges: B:K.16 pi-Cation interactions: B:R.140

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

ANP.5: 16 residues within 4Å: Chain A: D.12, R.13, A.14, G.15, K.16, S.17, T.18, R.94, R.140, A.177, K.179, S.180, I.181 Ligands: MG.1, FDM.3, ADP.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.13, A:G.15, A:K.16, A:K.16, A:S.17, A:T.18, A:T.18, A:R.94, A:R.140, A:R.140, A:K.179 Water bridges: A:S.17, A:S.17, A:S.17, A:S.17, A:Q.19, A:R.21 pi-Cation interactions: A:R.140 ANP.10: 16 residues within 4Å: Chain B: D.12, R.13, A.14, G.15, K.16, S.17, T.18, R.94, R.140, A.177, K.179, S.180, I.181 Ligands: MG.6, FDM.8, ADP.9 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:D.12, B:R.13, B:G.15, B:K.16, B:K.16, B:S.17, B:T.18, B:T.18, B:R.94, B:R.140, B:R.140, B:K.179 Water bridges: B:S.17, B:S.17, B:S.17, B:S.17, B:Q.19, B:R.21 pi-Cation interactions: B:R.140

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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