SMTL ID : 4fws.1

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with CTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: V.37, A.38, T.39, C.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.37 EDO.2: 4 residues within 4Å: Chain A: S.27, H.131, R.249, K.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.27, A:R.249, A:N.277, A:K.278 EDO.3: 3 residues within 4Å: Chain A: N.219, T.248, R.249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.219, A:R.249 Water bridges: A:R.249 EDO.4: 2 residues within 4Å: Chain A: E.175, S.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.179 EDO.6: 4 residues within 4Å: Chain B: V.37, A.38, T.39, C.40 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.37 EDO.7: 4 residues within 4Å: Chain B: S.27, H.131, R.249, K.278 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.27, B:R.249, B:N.277, B:K.278 EDO.8: 3 residues within 4Å: Chain B: N.219, T.248, R.249 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.219, B:R.249 Water bridges: B:R.249 EDO.9: 2 residues within 4Å: Chain B: E.175, S.179 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.179

2 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.5: 13 residues within 4Å: Chain A: H.188, H.216, G.218, N.219, G.220, S.290, D.291, L.292, R.293, G.338, G.339, I.340, N.343 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.219, A:N.219, A:G.220, A:S.290, A:L.292, A:R.293, A:R.293, A:R.293, A:G.339, A:I.340 Salt bridges: A:K.31, A:H.216 pi-Cation interactions: A:R.293 CTP.10: 13 residues within 4Å: Chain B: H.188, H.216, G.218, N.219, G.220, S.290, D.291, L.292, R.293, G.338, G.339, I.340, N.343 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.219, B:N.219, B:G.220, B:S.290, B:L.292, B:R.293, B:R.293, B:R.293, B:G.339, B:I.340 Salt bridges: B:K.31, B:H.216 pi-Cation interactions: B:R.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chittori, S. et al., Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies. Biochim.Biophys.Acta (2013)

Release Date

2013-06-19

Peptides

Propionate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Propionate kinase

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