SMTL ID : 5zdn.1 (1 other biounit)

The complex structure of FomD with CDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

monomer

Ligands

1 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.1: 10 residues within 4Å: Chain A: L.58, W.72, F.75, R.78, W.79, Q.80, S.81, K.146 Ligands: MG.4, MG.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.72, A:F.75, A:W.79 Hydrogen bonds: A:R.78, A:Q.80, A:S.81, A:S.81 Water bridges: A:W.72, A:K.146, A:D.147 Salt bridges: A:K.146 pi-Stacking: A:F.75

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: E.131, D.133, K.146, D.147 Ligands: MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.131, A:E.131, A:D.133, A:D.147, H2O.2 MG.3: 4 residues within 4Å: Chain A: N.113, D.129, D.133 Ligands: MG.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.129, A:D.133, H2O.1, H2O.2, H2O.2 MG.4: 2 residues within 4Å: Chain A: K.146 Ligands: CDP.1 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: K.150 Ligands: CDP.1 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: R.24, D.26, I.34, Y.36, H.70, W.72, W.97, N.113, D.129 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.36, A:Y.36, A:W.72 Water bridges: A:R.24, A:R.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sato, S. et al., Biochemical and Structural Analysis of FomD That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis. Biochemistry (2018)

Release Date

2018-07-25

Peptides

FomD: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

FomD

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