SMTL ID : 7vu9.1 (1 other biounit)

Pholiota squarrosa lectin (PhoSL) in complex with fucose(alpha1-6)[GlcNAc(beta1-4)]GlcNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 11 residues within 4Å: Chain A: A.1, V.3, L.21, Y.23, W.28 Chain B: D.11, G.12, D.13, Y.15, V.36 Ligands: FMT.4 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.21, B:Y.15, B:V.36 Hydrogen bonds: A:A.1, A:A.1, B:G.12, B:D.13, B:D.13, B:G.12, B:Y.15, B:Y.15 NAG-NAG-FUC.2: 11 residues within 4Å: Chain B: A.1, V.3, L.21, Y.23, W.28 Chain C: D.11, G.12, D.13, Y.15, V.36 Ligands: FMT.5 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.12, C:D.13, C:D.13, B:A.1, C:G.12, C:Y.15, C:Y.15 Hydrophobic interactions: B:L.21, C:Y.15, C:V.36, B:W.28 NAG-NAG-FUC.3: 11 residues within 4Å: Chain A: C.10, D.11, G.12, D.13, Y.15, V.36 Chain C: A.1, V.3, Y.23, W.28 Ligands: FMT.6 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.12, A:D.13, C:A.1, C:A.1, A:G.12, A:Y.15, A:Y.15 Hydrophobic interactions: C:V.3, C:Y.23, A:Y.15, A:V.36, C:W.28

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 5 residues within 4Å: Chain A: Y.23, G.24, D.25, W.28 Ligands: NAG-NAG-FUC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.25 FMT.5: 5 residues within 4Å: Chain B: Y.23, G.24, D.25, W.28 Ligands: NAG-NAG-FUC.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.25 FMT.6: 5 residues within 4Å: Chain C: Y.23, G.24, D.25, W.28 Ligands: NAG-NAG-FUC.3 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.25, C:D.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamasaki, K. et al., Core fucose-specific Pholiota squarrosa lectin (PhoSL) as a potent broad-spectrum inhibitor of SARS-CoV-2 infection. Febs J. (2023)

Release Date

2022-10-12

Peptides

Lectin (PhoSL): ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Lectin (PhoSL)

Related Entries With Identical Sequence