SMTL ID : 3ues.1

Crystal structure of alpha-1,3/4-fucosidase from Bifidobacterium longum subsp. infantis complexed with deoxyfuconojirimycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x DFU: (2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL(Non-covalent)

DFU.1: 12 residues within 4Å: Chain A: F.34, H.36, W.47, H.85, H.86, Y.131, D.172, A.174, E.217, D.283, W.290 Ligands: EDO.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.34, A:W.290 Hydrogen bonds: A:W.47, A:H.85, A:Y.131, A:D.172, A:D.172 DFU.4: 12 residues within 4Å: Chain B: F.34, H.36, W.47, H.85, H.86, Y.131, D.172, A.174, E.217, D.283, W.290 Ligands: EDO.5 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.34, B:W.290 Hydrogen bonds: B:W.47, B:H.85, B:D.172

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: W.170, D.172, G.173, A.174, V.206, W.213, E.217 Ligands: DFU.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.173, A:A.174, A:E.217 Water bridges: A:G.173, A:E.237 EDO.5: 8 residues within 4Å: Chain B: W.170, D.172, G.173, A.174, V.206, W.213, E.217 Ligands: DFU.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.172, B:G.173, B:A.174, B:E.217 Water bridges: B:G.173, B:E.237

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: H.372, D.375, N.377, T.380, S.471 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.372, A:N.377, A:T.380, A:T.380 Water bridges: A:G.376 NA.6: 5 residues within 4Å: Chain B: H.372, D.375, N.377, T.380, S.471 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.377, B:T.380, B:T.380 Water bridges: B:G.376

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakurama, H. et al., 1,3-1,4-alpha-L-fucosynthase that specifically introduces Lewis a/x antigens into type-1/2 chains. J.Biol.Chem. (2012)

Release Date

2012-04-04

Peptides

Alpha-1,3/4-fucosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-1,3/4-fucosidase