SMTL ID : 4h8e.1

Structure of S. aureus undecaprenyl diphosphate synthase in complex with FPP and sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.33, R.37 Ligands: FPP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.33, H2O.1, H2O.2, H2O.7 MG.4: 3 residues within 4Å: Chain B: D.33, R.37 Ligands: FPP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.33, H2O.2, H2O.7, H2O.7

2 x FPP: FARNESYL DIPHOSPHATE(Non-covalent)

FPP.2: 19 residues within 4Å: Chain A: M.32, D.33, G.34, N.35, G.36, R.37, R.46, H.50, M.54, I.57, A.76, R.84, E.88, L.95, P.96, F.99, F.148 Chain B: R.249 Ligands: MG.1 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.50, A:I.57, A:A.76, A:L.95, A:L.95, A:P.96, A:F.99, A:F.148, A:F.148 Hydrogen bonds: A:D.33, A:G.34, A:N.35, A:G.36, A:R.37, B:R.249 Water bridges: A:K.40, A:R.46, A:R.46, A:R.46, A:R.201 Salt bridges: A:R.37, A:R.46, A:R.46, A:H.50, A:R.84 FPP.5: 19 residues within 4Å: Chain A: R.249 Chain B: M.32, D.33, G.34, N.35, G.36, R.37, R.46, H.50, M.54, I.57, A.76, R.84, E.88, L.95, P.96, F.99, F.148 Ligands: MG.4 24 PLIP interactions: 23 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.50, B:I.57, B:A.76, B:L.95, B:L.95, B:P.96, B:F.99, B:F.148, B:F.148 Hydrogen bonds: B:G.34, B:N.35, B:G.36, B:R.37, A:R.249 Water bridges: B:K.40, B:R.46, B:R.46, B:R.46, B:R.201 Salt bridges: B:R.37, B:R.46, B:R.46, B:H.50, B:R.84

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

SO4.3: 7 residues within 4Å: Chain A: R.201, R.207, S.209 Chain B: Y.218, R.249, F.250, G.251 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.209, B:G.251 Water bridges: A:N.81, A:R.84, A:R.201, A:R.201, B:R.249, B:R.249, B:F.250, B:F.250 Salt bridges: A:R.201, A:R.207 SO4.6: 7 residues within 4Å: Chain A: Y.218, R.249, F.250, G.251 Chain B: R.201, R.207, S.209 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.209, A:G.251 Water bridges: B:R.84, B:R.201, B:R.201, A:Y.218, A:R.249, A:R.249, A:F.250, A:F.250 Salt bridges: B:R.201, B:R.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, W. et al., Antibacterial drug leads targeting isoprenoid biosynthesis. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2012-12-19

Peptides

Undecaprenyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Undecaprenyl pyrophosphate synthase

Related Entries With Identical Sequence