SMTL ID : 6fx1.1 (3 other biounits)

Crystal structure of Pholiota squarrosa lectin in complex with an octasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

2 x C4W- NAG- BMA- MAN- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamine(Non-covalent)

C4W-NAG-BMA-MAN-NAG-FUC.1: 12 residues within 4Å: Chain A: D.14, G.15, D.16, Y.18, T.37, N.38, V.39 Chain B: A.4, L.24, F.26, W.31 Ligands: MLI.6 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.24, B:F.26 Hydrogen bonds: B:A.4, A:G.15, A:D.16 Water bridges: A:Y.18, A:D.36 C4W-NAG-BMA-MAN-NAG-FUC.3: 12 residues within 4Å: Chain A: A.4, L.24, F.26, W.31 Chain C: D.14, G.15, D.16, Y.18, T.37, N.38, V.39 Ligands: MLI.4 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:G.15, C:D.16, A:A.4 Hydrophobic interactions: A:L.24, A:F.26

1 x C4W- NAG- BMA- MAN- NAG- MAN- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamine(Non-covalent)

C4W-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2: 13 residues within 4Å: Chain B: D.14, G.15, D.16, Y.18, D.36, T.37, N.38, V.39 Chain C: A.4, L.24, F.26, W.31 Ligands: MLI.7 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:D.16, C:A.4, B:G.15, B:D.16 Hydrophobic interactions: C:L.24, C:F.26 Water bridges: B:N.38

3 x MLI: MALONATE ION(Non-covalent)(Non-functional Binders)

MLI.4: 7 residues within 4Å: Chain A: Q.34, W.35, D.36 Chain C: D.36, T.37, N.38 Ligands: C4W-NAG-BMA-MAN-NAG-FUC.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.36 Water bridges: A:K.19, A:D.36 Hydrophobic interactions: C:D.36 MLI.6: 7 residues within 4Å: Chain A: D.36, T.37, N.38 Chain B: Q.34, W.35, D.36 Ligands: C4W-NAG-BMA-MAN-NAG-FUC.1 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.36, A:N.38 Salt bridges: B:K.19 MLI.7: 7 residues within 4Å: Chain B: D.36, T.37, N.38 Chain C: Q.34, W.35, D.36 Ligands: C4W-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:N.38, C:D.36 Water bridges: B:D.36, C:D.36, C:D.36, C:D.36

1 x OOA: 3-OXOOCTANOIC ACID(Non-covalent)

OOA.5: 2 residues within 4Å: Chain A: G.27, D.28 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.28

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Cabanettes, A. et al., Recognition of Complex Core-Fucosylated N-Glycans by a Mini Lectin. Angew. Chem. Int. Ed. Engl. (2018)

Release Date

2018-07-11

Peptides

lectin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

lectin

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