SMTL ID : 1mrn.1

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH BISUBSTRATE INHIBITOR (TP5A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 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 SO4.2: 8 residues within 4Å: Chain A: V.8, G.10, A.11, G.12, K.13, R.14, R.149, R.153 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13, A:R.14 Water bridges: A:K.13, A:K.13, A:T.15, A:R.149 Salt bridges: A:K.13, A:R.153 SO4.5: 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 SO4.6: 8 residues within 4Å: Chain B: V.8, G.10, A.11, G.12, K.13, R.14, R.149, R.153 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:K.13, B:R.14 Water bridges: B:K.13, B:K.13, B:T.15, B:R.149 Salt bridges: B:K.13, B:R.153

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.9, D.163, E.166 Ligands: T5A.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.9, A:E.166 MG.7: 4 residues within 4Å: Chain B: D.9, D.163, E.166 Ligands: T5A.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.9, B:E.166

2 x T5A: P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE(Non-covalent)

T5A.4: 22 residues within 4Å: Chain A: D.9, F.36, P.37, Y.39, D.46, A.49, E.50, L.52, H.53, E.55, 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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.36, A:Y.103 Hydrogen bonds: A:F.36, A:D.46, A:E.55, A:R.74, A:R.74, A:N.100 Water bridges: A:E.50, A:R.95, A:R.95, A:D.163 Salt bridges: A:R.95, A:R.160 pi-Stacking: A:H.53, A:F.70 T5A.8: 22 residues within 4Å: Chain B: D.9, F.36, P.37, Y.39, D.46, A.49, E.50, L.52, H.53, E.55, F.70, R.74, R.95, Y.96, S.99, N.100, Y.103, R.160, D.163, Y.165, E.166 Ligands: MG.7 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.36, B:Y.103 Hydrogen bonds: B:F.36, B:Y.39, B:D.46, B:R.74, B:R.74, B:N.100 Water bridges: B:R.95, B:R.95, B:D.163, B:D.163, B:D.163 Salt bridges: B:R.95, B:R.160 pi-Stacking: B:H.53, B:F.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haouz, A. et al., Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism. J.Biol.Chem. (2003)

Release Date

2003-01-07

Peptides

Thymidylate Kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thymidylate Kinase

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