SMTL ID : 4e5u.1

The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with thymidine monophosphate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.1: 15 residues within 4Å: Chain A: E.15, E.42, P.43, R.53, L.57, M.73, R.77, R.99, F.100, A.103, T.104, Y.107, Q.108, F.158 Ligands: CA.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.42, A:R.99, A:A.103, A:Y.107 Hydrogen bonds: A:R.77, A:Q.108, A:Q.108 Water bridges: A:R.41, A:R.53, A:R.53, A:R.53 Salt bridges: A:R.53, A:R.99 TMP.3: 15 residues within 4Å: Chain B: E.15, E.42, P.43, R.53, L.57, M.73, R.77, R.99, F.100, A.103, T.104, Y.107, Q.108, F.158 Ligands: CA.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:E.42, B:R.99, B:A.103, B:Y.107 Hydrogen bonds: B:R.77, B:Q.108, B:Q.108 Water bridges: B:R.41, B:R.53, B:R.53, B:R.53, B:R.53, B:R.99, B:R.99, B:D.156 Salt bridges: B:R.53, B:R.99

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: E.15, E.159 Ligands: TMP.1 6 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: A:E.15, A:E.159, TMP.1, H2O.83, H2O.84, H2O.99 CA.4: 3 residues within 4Å: Chain B: E.15, E.159 Ligands: TMP.3 6 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:E.15, B:E.159, TMP.3, H2O.141, H2O.204, H2O.205 CA.5: 2 residues within 4Å: Chain B: A.149, R.152 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.149, B:R.152, H2O.216, H2O.217, H2O.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with thymidine monophosphate. To be Published

Release Date

2012-03-28

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate kinase

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