SMTL ID : 4jfu.1 (1 other biounit)

Crystal structure of a bacterial fucosidase with iminosugar inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

1 x K80: (2S,3R,4S,5S)-2-methyl-5-(4-methylphenyl)pyrrolidine-3,4-diol(Non-covalent)

K80.1: 12 residues within 4Å: Chain A: H.32, E.53, W.54, H.101, H.102, Y.144, W.193, D.195, W.198, E.254, W.282 Ligands: GOL.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.54, A:W.193, A:W.198, A:W.282 Hydrogen bonds: A:H.32, A:E.53, A:W.54, A:D.195

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

SO4.2: 3 residues within 4Å: Chain A: R.228, R.237, H.238 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.228, A:R.237, A:H.238 SO4.3: 4 residues within 4Å: Chain A: K.56, V.61, P.62, A.63 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.63 Water bridges: A:K.56, A:K.56, A:D.64 Salt bridges: A:K.56

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 8 residues within 4Å: Chain A: A.29, I.31, W.83, M.86, A.87, Y.134, F.317, F.325 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:F.317 IMD.5: 5 residues within 4Å: Chain A: A.353, R.365, D.369, V.371, V.435 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.353, A:D.369 pi-Cation interactions: A:R.365

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: A.51, W.54, W.58, N.280 Ligands: K80.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.280 Water bridges: A:A.51, A:N.280 GOL.7: 4 residues within 4Å: Chain A: K.56, S.57, W.150, Y.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.56 Water bridges: A:K.56, A:K.56 GOL.8: 5 residues within 4Å: Chain A: N.135, G.138, I.139, D.140, K.190 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.138, A:K.190 Water bridges: A:N.135, A:N.135, A:K.190 GOL.9: 6 residues within 4Å: Chain A: K.111, Y.112, K.180, E.181, T.184, R.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.111, A:T.184 Water bridges: A:T.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hottin, A. et al., alpha-L-fucosidase inhibition by pyrrolidine-ferrocene hybrids: rationalization of ligand-binding properties by structural studies. Chemistry (2013)

Release Date

2013-09-18

Peptides

alpha-L-fucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

alpha-L-fucosidase

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