SMTL ID : 1mrs.1

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH 5-CH2OH DEOXYURIDINE MONOPHOSPHATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: A.154, 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 12 PLIP interactions: 12 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:K.13, A:K.13, A:K.13, A:R.153 Salt bridges: A:K.13, A:R.153 SO4.5: 4 residues within 4Å: Chain B: A.154, 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 12 PLIP interactions: 12 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:K.13, B:K.13, B:K.13 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: 5HU.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.9, A:E.166, H2O.1, H2O.1, H2O.1 MG.7: 4 residues within 4Å: Chain B: D.9, D.163, E.166 Ligands: 5HU.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.9, B:E.166, H2O.3, H2O.4, H2O.4

2 x 5HU: 5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE(Non-covalent)

5HU.4: 13 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 Ligands: MG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.103 Hydrogen bonds: A:F.36, A:R.74, A:R.74, A:N.100, A:D.163 Water bridges: A:R.95, A:R.95, A:R.160 Salt bridges: A:R.95 pi-Stacking: A:F.70 5HU.8: 13 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 Ligands: MG.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.103 Hydrogen bonds: B:D.9, B:F.36, B:Y.39, B:R.74, B:R.74, B:N.100, B:D.163 Water bridges: B:R.95, B:R.95, B:R.160 Salt bridges: B:R.95 pi-Stacking: 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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