SMTL ID : 1e2g.1

Human thymidylate kinase complexed with ADP, TDP and a magnesium-ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x TMP: THYMIDINE-5'-PHOSPHATE(Covalent)

TMP.1: 13 residues within 4Å: Chain A: D.18, F.45, P.46, L.60, F.75, R.79, R.100, S.104, G.105, F.108, Y.154 Ligands: TYD.3, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.45, A:F.108 Hydrogen bonds: A:R.48, A:R.79, A:R.79 Water bridges: A:R.19, A:K.22, A:K.22, A:S.76, A:R.100, A:R.100, A:G.105, A:Y.154 Salt bridges: A:K.22, A:R.100 pi-Stacking: A:F.75 TMP.6: 13 residues within 4Å: Chain B: D.18, F.45, P.46, L.60, F.75, R.79, R.100, S.104, G.105, F.108, Y.154 Ligands: TYD.8, MG.9 18 PLIP interactions: 18 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:R.19, B:K.22, B:K.22, B:S.76, B:R.100, B:R.100, B:R.100, B:G.105, B:T.109 Salt bridges: B:K.22, B:R.100 pi-Stacking: B:F.75

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

ADP.2: 15 residues within 4Å: Chain A: V.17, D.18, R.19, A.20, G.21, K.22, S.23, T.24, R.146, G.147, A.183, K.185, S.186, I.187 Ligands: MG.4 24 PLIP interactions: 24 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:R.19, A:R.19, A:R.19, A:R.19, A:R.19, A:R.146, A:R.146, A:G.147, A:G.147, A:I.187 Salt bridges: A:R.19, A:R.19, A:K.22 pi-Cation interactions: A:R.146, A:R.146 ADP.7: 15 residues within 4Å: Chain B: V.17, D.18, R.19, A.20, G.21, K.22, S.23, T.24, R.146, G.147, A.183, K.185, S.186, I.187 Ligands: MG.9 25 PLIP interactions: 25 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:R.19, B:R.19, B:R.19, B:R.19, B:R.100, B:R.100, B:R.146, B:R.146, B:G.147, B:G.147, B:I.187 Salt bridges: B:R.19, B:R.19, B:K.22 pi-Cation interactions: B:R.146, B:R.146

2 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.3: 15 residues within 4Å: Chain A: D.18, 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 Ligands: TMP.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.45 Hydrogen bonds: A:R.79, A:R.79 Water bridges: A:R.19, A:R.19, A:R.19, A:R.48, A:S.76, A:R.100, A:R.100, A:R.100, A:G.105, A:T.109, A:Y.154, A:E.155 Salt bridges: A:R.48, A:R.48, A:R.100 pi-Stacking: A:F.75 TYD.8: 15 residues within 4Å: Chain B: D.18, 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 Ligands: TMP.6 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.45 Hydrogen bonds: B:R.79, B:R.79 Water bridges: B:R.19, B:R.19, B:R.48, B:S.76, B:R.100, B:R.100, B:R.100, B:G.105, B:T.109, B:T.109, B:T.109, B:E.155, B:E.155 Salt bridges: B:R.48, B:R.48, B:R.100 pi-Stacking: B:F.75

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

MG.4: 3 residues within 4Å: Chain A: S.23 Ligands: TMP.1, ADP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.23, H2O.5, H2O.10, H2O.10, H2O.11 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: TMP.6, ADP.7 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.23, H2O.16, H2O.21, H2O.21, H2O.21 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., Insights Into the Phosphoryltransfer Mechanism of Human Thymidylate Kinase Gained from Crystal Structures of Enzyme Complexes Along the Reaction Coordinate. Structure (2000)

Release Date

2001-05-17

Peptides

THYMIDYLATE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

THYMIDYLATE KINASE

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