SMTL ID : 3hjn.1

Crystal structure of thymidylate kinase in complex with dTDP and ADP from Thermotoga maritima

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: I.8, D.9, G.10, S.11, G.12, K.13, S.14, T.15, R.138, K.139, G.174, R.176, S.177, I.178, I.181 Ligands: TYD.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.10, A:S.11, A:G.12, A:K.13, A:S.14, A:T.15, A:T.15, A:T.15, A:R.138, A:R.138, A:R.176 Water bridges: A:S.14, A:Q.16 Salt bridges: A:K.13, A:K.139, A:K.139 pi-Cation interactions: A:R.138, A:R.138 ADP.4: 14 residues within 4Å: Chain B: I.8, G.10, S.11, G.12, K.13, S.14, T.15, R.138, G.174, R.176, S.177, I.178, I.181 Ligands: TYD.5 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.10, B:S.11, B:G.12, B:K.13, B:S.14, B:T.15, B:T.15, B:T.15, B:R.176 Water bridges: B:K.13, B:S.14 Salt bridges: B:K.13 pi-Cation interactions: B:R.138

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

TYD.2: 16 residues within 4Å: Chain A: D.9, K.13, E.36, R.47, F.64, R.68, R.89, S.93, S.94, Y.97, Q.98, K.139, N.143, F.145 Ligands: ADP.1, MG.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:E.36, A:Y.97 Hydrogen bonds: A:D.9, A:R.68, A:Q.98, A:Q.98, A:N.143, A:N.143 Water bridges: A:S.14, A:S.14, A:S.14, A:S.14, A:R.47, A:R.47 Salt bridges: A:K.13, A:R.47, A:R.89, A:R.89, A:K.139 pi-Stacking: A:F.64 TYD.5: 16 residues within 4Å: Chain B: D.9, G.10, K.13, E.36, P.37, R.47, F.64, R.68, R.89, S.93, S.94, Y.97, Q.98, N.143, F.145 Ligands: ADP.4 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:E.36, B:F.64, B:Y.97 Hydrogen bonds: B:D.9, B:D.9, B:G.10, B:R.68, B:Q.98, B:Q.98, B:N.143, B:N.143 Water bridges: B:K.13, B:S.14 Salt bridges: B:K.13, B:R.47, B:R.89, B:R.89 pi-Stacking: B:F.64

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.14, D.88, K.139 Ligands: ADP.1, TYD.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.14, H2O.2, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshikawa, S. et al., Crystal structure of thymidylate kinase in complex with dTDP and ADP from Thermotoga maritima. To be Published

Release Date

2009-06-02

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate kinase