SMTL ID : 4jl2.2 (1 other biounit)

Crystal structure of a bacterial fucosidase with a monovalent iminocyclitol inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x LM5: (3S,4R,5S)-N-benzyl-3,4-dihydroxy-5-methyl-D-prolinamide(Non-covalent)

LM5.1: 12 residues within 4Å: Chain A: H.32, E.53, W.54, H.101, Y.144, W.193, D.195, W.198, R.228, E.254, R.255, W.282 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.193, A:W.282 Hydrogen bonds: A:H.32, A:W.54, A:W.54, A:Y.144, A:D.195, A:D.195, A:R.228

5 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 8 residues within 4Å: Chain A: A.29, I.31, W.83, M.86, A.87, Y.134, F.317, F.325 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.134, A:Y.134 pi-Stacking: A:F.317 IMD.3: 2 residues within 4Å: Chain A: Y.6, W.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.6 pi-Stacking: A:W.207, A:W.207 IMD.4: 9 residues within 4Å: Chain A: T.388, I.392, T.393, E.410, T.412, R.413, N.414, E.415, Y.416 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.392, A:E.410 Water bridges: A:N.414 IMD.5: 3 residues within 4Å: Chain A: K.56, P.62, A.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.63 Water bridges: A:K.56, A:D.64 IMD.6: 2 residues within 4Å: Chain A: G.49, G.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.49 Water bridges: A:G.50

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

SO4.7: 4 residues within 4Å: Chain A: W.198, R.228, R.237, H.238 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.228, A:R.237 Salt bridges: A:R.228, A:R.237, A:H.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moreno-Clavijo, E. et al., Exploring a Multivalent Approach to alpha-L-Fucosidase Inhibition. EUR.J.ORG.CHEM. (2013)

Release Date

2014-01-22

Peptides

alpha-L-fucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

alpha-L-fucosidase

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