SMTL ID : 4edh.1

The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with ADP,TMP and Mg.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

homo-dimer

Ligands

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

TMP.1: 13 residues within 4Å: Chain A: E.42, P.43, R.53, M.73, R.77, R.99, F.100, A.103, T.104, Y.107, Q.108, F.158 Ligands: MG.3 16 PLIP interactions: 16 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:E.15, A:S.20, A:R.41, A:D.98, A:D.98, A:R.99, A:R.99 Salt bridges: A:R.53, A:R.99 TMP.6: 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: MG.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:E.42, B:R.99, B:A.103, B:Y.107 Hydrogen bonds: B:E.15, B:R.77, B:Q.108, B:Q.108 Water bridges: B:S.20, B:S.20, B:R.53, B:R.53, B:R.53, B:R.53, B:D.98, B:D.98, B:D.98, B:R.99 Salt bridges: B:R.53, B:R.99

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

ADP.2: 15 residues within 4Å: Chain A: P.14, E.15, G.16, A.17, G.18, K.19, S.20, T.21, R.148, A.189, L.191, P.192, L.193, V.196 Ligands: MG.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:P.14, A:G.16, A:A.17, A:G.18, A:K.19, A:S.20, A:T.21, A:T.21, A:T.21, A:R.148, A:R.148, A:L.191, A:L.193 Water bridges: A:E.15, A:E.15, A:E.15, A:E.15, A:S.20, A:S.20, A:N.22 Salt bridges: A:K.19 pi-Cation interactions: A:R.148 ADP.7: 13 residues within 4Å: Chain B: G.16, A.17, G.18, K.19, S.20, T.21, R.148, A.189, L.191, P.192, L.193, V.196 Ligands: MG.8 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:P.14, B:G.16, B:A.17, B:G.18, B:K.19, B:S.20, B:T.21, B:T.21, B:T.21, B:R.148, B:R.148, B:L.191, B:L.193 Water bridges: B:K.19, B:S.20, B:N.22 Salt bridges: B:K.19 pi-Cation interactions: B:R.148

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.20, D.98 Ligands: TMP.1, ADP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.20, H2O.3, H2O.8, H2O.8, H2O.8 MG.8: 4 residues within 4Å: Chain B: S.20, D.98 Ligands: TMP.6, ADP.7 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.20, H2O.17, H2O.17, H2O.17, H2O.17

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 3 residues within 4Å: Chain A: P.141, D.188, G.190 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.188, A:G.190 Water bridges: A:R.170, A:R.170, A:R.170, A:R.170

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

SO4.5: 2 residues within 4Å: Chain A: R.131, R.183 7 PLIP interactions: 7 interactions with chain A Water bridges: A:E.123, A:R.176, A:R.176, A:R.183, A:R.183 Salt bridges: A:R.131, A:R.183

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 2 residues within 4Å: Chain B: R.41, R.53 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.41, B:R.41 Water bridges: B:R.53

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 ADP,TMP and Mg. To be Published

Release Date

2012-05-23

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate kinase

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