SMTL ID : 1n5j.1

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE DIPHOSPHATE (TDP) AND THYMIDINE TRIPHOSPHATE (TTP) AT PH 5.4 (1.85 A RESOLUTION)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: V.8, G.10, A.11, G.12, K.13, R.14, R.149, R.153 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13, A:R.14 Water bridges: A:D.9, A:G.12, A:K.13, A:K.13, A:K.13, A:T.15, A:R.153 Salt bridges: A:K.13, A:R.153 SO4.2: 5 residues within 4Å: Chain A: A.154, Q.155, A.161, R.162, R.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.162 Salt bridges: A:R.162, A:R.167 SO4.6: 8 residues within 4Å: Chain B: V.8, G.10, A.11, G.12, K.13, R.14, R.149, R.153 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:K.13, B:R.14 Water bridges: B:D.9, B:D.9, B:D.9, B:G.12, B:K.13, B:K.13, B:T.15 Salt bridges: B:K.13, B:R.153 SO4.7: 5 residues within 4Å: Chain B: A.154, Q.155, A.161, R.162, R.167 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.162 Salt bridges: B:R.162, B:R.167

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.9, E.166 Ligands: TYD.4, TTP.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.9, A:E.166, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain B: D.9, E.166 Ligands: TYD.9, TTP.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.9, B:E.166, H2O.7, H2O.7

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

TYD.4: 15 residues within 4Å: Chain A: D.9, F.36, P.37, Y.39, L.52, F.70, R.74, R.95, S.99, N.100, Y.103, Y.165, E.166 Ligands: MG.3, TTP.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.37, A:Y.103 Hydrogen bonds: A:Y.39, A:R.74, A:R.74, A:N.100 Water bridges: A:D.9, A:R.14, A:R.14, A:R.14, A:R.14, A:R.95, A:E.166, A:E.166 Salt bridges: A:R.95 pi-Stacking: A:F.70 TYD.9: 15 residues within 4Å: Chain B: D.9, F.36, P.37, Y.39, L.52, F.70, R.74, R.95, S.99, N.100, Y.103, Y.165, E.166 Ligands: MG.8, TTP.10 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.37, B:Y.103 Hydrogen bonds: B:Y.39, B:Y.39, B:R.74, B:R.74, B:N.100 Water bridges: B:D.9, B:D.9, B:D.9, B:R.14, B:R.14, B:R.14, B:R.14, B:D.163, B:D.163, B:D.163, B:E.166 Salt bridges: B:R.95 pi-Stacking: B:F.70

2 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.5: 18 residues within 4Å: Chain A: D.9, R.14, F.36, P.37, Y.39, F.70, R.74, R.95, Y.96, S.99, N.100, Y.103, R.160, D.163, Y.165, E.166 Ligands: MG.3, TYD.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.36, A:Y.103 Hydrogen bonds: A:R.74, A:R.74, A:N.100 Water bridges: A:D.9, A:R.14, A:R.14, A:R.14, A:R.14, A:F.36, A:R.95, A:R.160, A:E.166, A:E.166 Salt bridges: A:R.14, A:R.95, A:R.160 pi-Stacking: A:F.70 TTP.10: 18 residues within 4Å: Chain B: D.9, R.14, F.36, P.37, Y.39, F.70, R.74, R.95, Y.96, S.99, N.100, Y.103, R.160, D.163, Y.165, E.166 Ligands: MG.8, TYD.9 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:F.36, B:Y.103 Hydrogen bonds: B:Y.39, B:R.74, B:R.74, B:N.100 Water bridges: B:D.9, B:D.9, B:D.9, B:R.14, B:R.14, B:R.14, B:R.14, B:F.36, B:R.153, B:R.160, B:D.163, B:D.163 Salt bridges: B:R.14, B:R.95, B:R.160 pi-Stacking: B:F.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fioravanti, E. et al., Mycobacterium tuberculosis Thymidylate Kinase: Structural Studies of Intermediates along the Reaction Pathway. J.Mol.Biol. (2003)

Release Date

2003-04-15

Peptides

THYMIDYLATE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

THYMIDYLATE KINASE

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