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

Crystal Structure of alpha-L-fucosidase from Fusarium graminearum in the open form in complex with L-fucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: N.280, V.296, R.297, P.298, T.523, K.549, T.551, F.553, R.557, F.558, T.559, S.562, V.581 Ligands: TRS.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.557 Water bridges: A:R.557

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.2: 5 residues within 4Å: Chain A: D.230, P.232, E.246, Q.247, R.249 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.246, A:E.246

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 5 residues within 4Å: Chain A: P.386, N.387, N.401, S.402, S.403 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.387, A:N.387, A:N.401 Water bridges: A:N.401, A:S.403, A:S.403, A:S.403 NAG.4: 1 residues within 4Å: Chain A: N.187 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.187

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 11 residues within 4Å: Chain A: R.297, A.378, W.379, D.380, R.409, D.413, I.495, G.516, V.517, A.532, G.533 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.379, A:W.379, A:R.409, A:R.409, A:A.532 Water bridges: A:R.297, A:R.297, A:D.413, A:I.495, A:I.495 TRS.6: 10 residues within 4Å: Chain A: Y.271, K.272, H.273, H.274, D.275, H.276, F.278, N.280, D.285 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.271, A:N.280, A:D.285 Water bridges: A:H.276, A:F.278 TRS.7: 8 residues within 4Å: Chain A: S.402, S.403, P.424, E.425, D.426, L.428, V.429, S.430 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.402, A:D.426, A:S.430, A:S.430 Water bridges: A:S.403, A:S.403

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

NA.8: 7 residues within 4Å: Chain A: D.15, K.16, H.17, N.18, A.19, T.281, S.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.17

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: S.45, E.46, W.47, W.311 Ligands: FUL.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.46 Water bridges: A:S.45, A:W.311 GOL.10: 4 residues within 4Å: Chain A: S.462, E.463, W.464, E.465 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.464 Water bridges: A:W.464, A:E.465, A:E.465, A:E.465

1 x FUL: beta-L-fucopyranose(Non-covalent)

FUL.11: 14 residues within 4Å: Chain A: Y.32, H.34, E.46, W.47, H.126, H.127, H.171, W.224, D.226, F.227, K.272, D.303, W.311 Ligands: GOL.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.311 Hydrogen bonds: A:H.34, A:E.46, A:W.47, A:H.126, A:H.127, A:D.226 Water bridges: A:D.226, A:K.272 Salt bridges: A:K.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, H. et al., Structure and Substrate Specificity of a Eukaryotic Fucosidase from Fusarium graminearum. J.Biol.Chem. (2014)

Release Date

2014-03-19

Peptides

Alpha-fucosidase GH29: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-fucosidase GH29

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