SMTL ID : 3sgv.1

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1290

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

5 x 2BJ: 2-{[3-(3,4-dimethylphenoxy)phenyl]carbamoyl}-4-nitrobenzoic acid(Covalent)(Non-covalent)

2BJ.1: 12 residues within 4Å: Chain A: H.43, K.44, A.47, K.48, V.50, R.51, L.85, L.88, W.91, A.92, E.96 Ligands: 2BJ.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:K.44, A:K.44, A:A.47, A:V.50, A:R.51, A:L.85, A:L.88, A:L.88, A:L.88, A:W.91, A:A.92, A:E.96, A:E.96 Hydrogen bonds: A:K.48 Water bridges: A:R.51, A:R.51 Salt bridges: A:K.48, A:R.51 2BJ.2: 15 residues within 4Å: Chain A: M.25, D.26, G.27, N.28, G.29, R.39, H.43, G.46, A.47, V.50, A.69, L.85, F.89, I.141 Ligands: 2BJ.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.85, A:L.85, A:F.89, A:F.89 Hydrogen bonds: A:G.27, A:N.28, A:N.28, A:G.29, A:R.39 Water bridges: A:R.30 2BJ.3: 21 residues within 4Å: Chain B: I.24, M.25, D.26, G.27, N.28, G.29, R.39, H.43, A.47, Y.68, A.69, F.70, S.71, E.73, N.74, F.89, A.92, R.194, W.221 Ligands: 2BJ.4, 2BJ.5 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:M.25, B:D.26, B:H.43, B:A.47, B:A.69, B:F.89, B:A.92 Hydrogen bonds: B:M.25, B:G.27, B:N.28, B:G.29, B:R.39, B:E.73, B:N.74 Water bridges: B:D.26, B:R.30 Salt bridges: B:R.39 2BJ.4: 19 residues within 4Å: Chain B: M.25, V.50, L.67, A.69, F.70, W.75, L.85, M.86, F.89, L.93, E.96, R.115, F.116, I.141, A.142, A.143, N.144 Ligands: 2BJ.3, 2BJ.5 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.50, B:A.69, B:W.75, B:W.75, B:F.89, B:F.89, B:L.93, B:E.96, B:I.141, B:I.141 Hydrogen bonds: B:A.142, B:N.144 Water bridges: B:F.70, B:F.70, B:Y.145, B:Y.145 pi-Stacking: B:F.89 2BJ.5: 6 residues within 4Å: Chain B: H.43, W.75, L.85, L.88 Ligands: 2BJ.3, 2BJ.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.43, B:W.75, B:L.85, B:L.88, B:L.88

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
B

B
A

Undecaprenyl pyrophosphate synthase

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