SMTL ID : 2e20.1

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x B4P: BIS(ADENOSINE)-5'-TETRAPHOSPHATE(Non-covalent)

B4P.1: 24 residues within 4Å: Chain A: N.24, R.99, A.101, A.128, H.131, F.187, H.188, H.216, G.218, N.219, G.220, P.240, R.249, S.290, D.291, L.292, R.293, E.296, G.338, G.339, I.340, N.343, S.344 Ligands: EDO.2 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:N.24, A:R.99, A:N.219, A:N.219, A:N.219, A:G.220, A:G.220, A:R.249, A:D.291, A:L.292, A:R.293, A:R.293, A:G.339, A:I.340, A:N.343 Water bridges: A:R.99, A:R.99, A:H.131, A:H.131, A:H.131, A:N.135, A:N.277 Salt bridges: A:K.31, A:H.188, A:H.188, A:H.216 pi-Stacking: A:H.131, A:H.131, A:F.187 pi-Cation interactions: A:R.293 B4P.3: 24 residues within 4Å: Chain B: N.24, R.99, A.101, A.128, H.131, F.187, H.188, H.216, G.218, N.219, G.220, P.240, R.249, S.290, D.291, L.292, R.293, E.296, G.338, G.339, I.340, N.343, S.344 Ligands: EDO.4 29 PLIP interactions: 29 interactions with chain B Hydrogen bonds: B:N.24, B:R.99, B:N.219, B:N.219, B:N.219, B:G.220, B:G.220, B:R.249, B:D.291, B:L.292, B:R.293, B:R.293, B:G.339, B:I.340, B:N.343 Water bridges: B:R.99, B:R.99, B:H.131, B:H.131, B:N.135, B:N.277 Salt bridges: B:K.31, B:H.188, B:H.188, B:H.216 pi-Stacking: B:H.131, B:H.131, B:F.187 pi-Cation interactions: B:R.293

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

EDO.2: 7 residues within 4Å: Chain A: F.187, H.188, G.220, M.236, P.240, R.249 Ligands: B4P.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.249, A:R.249 Water bridges: A:H.188 EDO.4: 7 residues within 4Å: Chain B: F.187, H.188, G.220, M.236, P.240, R.249 Ligands: B4P.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.249, B:R.249 Water bridges: B:H.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Simanshu, D.K. et al., Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity. Proteins (2008)

Release Date

2007-09-18

Peptides

Propionate Kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Propionate Kinase

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