SMTL ID : 4j28.1 (1 other biounit)

Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in complex with a 5-membered iminocyclitol inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x EAT: (2S,3S,4R,5S)-2-(1H-benzimidazol-2-yl)-5-methylpyrrolidine-3,4-diol(Non-covalent)

EAT.1: 13 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: IMD.3, IMD.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.54, A:W.193, A:W.198, A:W.282 Hydrogen bonds: A:E.53, A:E.53, A:H.101, A:H.102, A:E.254 pi-Stacking: A:W.54

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 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:F.317 IMD.3: 3 residues within 4Å: Chain A: W.54, W.58 Ligands: EAT.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.280 pi-Stacking: A:W.54, A:W.54, A:W.58 IMD.4: 5 residues within 4Å: Chain A: E.254, T.276, E.279, N.280, W.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.276 Water bridges: A:T.276 IMD.5: 3 residues within 4Å: Chain A: W.198 Ligands: EAT.1, SO4.7 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:W.198 IMD.6: 5 residues within 4Å: Chain A: R.365, D.369, V.371, I.392, V.435 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:R.365

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

SO4.7: 5 residues within 4Å: Chain A: W.198, R.228, R.237, H.238 Ligands: IMD.5 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.228, A:R.237, A:H.238 SO4.8: 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 SO4.9: 5 residues within 4Å: Chain A: K.111, Y.112, K.180, E.181, T.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.184 Water bridges: A:Y.112 Salt bridges: A:K.111

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: N.135, G.138, I.139, D.140, T.188, K.190 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.135, A:G.138, A:D.140, A:V.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wright, D.W. et al., Three dimensional structure of a bacterial alpha-l-fucosidase with a 5-membered iminocyclitol inhibitor. Bioorg.Med.Chem. (2013)

Release Date

2013-05-08

Peptides

Alpha-L-fucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-L-fucosidase

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