SMTL ID : 6zfc.2 (1 other biounit)

Fucose-binding lectin from Burkholderia ambifaria (BamBL) in complex with a fucosyl derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-trimer

Ligands

6 x QJB: 2-[(2~{S},3~{S},4~{R},4~{a}~{S},10~{a}~{S})-2-methyl-3,4-bis(oxidanyl)-3,4,4~{a},10~{a}-tetrahydro-2~{H}-pyrano[2,3-b][1,4]benzoxathiin-7-yl]-~{N}-(3-oxidanylpropyl)ethanamide(Non-covalent)

QJB.1: 10 residues within 4Å: Chain A: R.15, E.26, Y.35, G.37, A.38, F.39, V.57, I.59, W.74, W.79 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.57, A:I.59 Hydrogen bonds: A:R.15, A:A.38, A:F.39 Salt bridges: A:R.15 pi-Stacking: A:W.74 QJB.2: 10 residues within 4Å: Chain A: W.51, R.60, E.71, G.82, A.83, Y.84 Chain B: P.12, I.14, Y.29, W.34 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.51, B:I.14, B:Y.29 Hydrogen bonds: A:A.83, A:Y.84 Salt bridges: A:R.60 QJB.3: 9 residues within 4Å: Chain B: R.15, E.26, Y.35, G.37, A.38, F.39, I.59, W.74, W.79 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.59, B:W.74 Hydrogen bonds: B:A.38, B:F.39 Salt bridges: B:R.15 QJB.4: 10 residues within 4Å: Chain B: W.51, R.60, E.71, G.82, A.83, Y.84 Chain C: P.12, I.14, Y.29, W.34 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:I.14, C:Y.29, B:W.51, B:A.83 Hydrogen bonds: B:A.83, B:Y.84 Salt bridges: B:R.60 QJB.5: 10 residues within 4Å: Chain A: P.12, I.14, Y.29, W.34 Chain C: W.51, R.60, E.71, G.82, A.83, Y.84 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:I.14, A:Y.29, C:W.51, C:A.83 Water bridges: A:Y.29 Hydrogen bonds: C:A.83, C:Y.84 Salt bridges: C:R.60 QJB.6: 10 residues within 4Å: Chain C: R.15, E.26, Y.35, G.37, A.38, F.39, V.57, I.59, W.74, W.79 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.38, C:V.57, C:I.59, C:W.74 Hydrogen bonds: C:R.15, C:A.38, C:F.39 Salt bridges: C:R.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuhaudomlarp, S. et al., Fucosylated ubiquitin and orthogonally glycosylated mutant A28C: conceptually new ligands for Burkholderia ambifaria lectin (BambL). Chem Sci (2020)

Release Date

2020-10-28

Peptides

bacterial lectin from Burkholderia ambifaria: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

bacterial lectin from Burkholderia ambifaria

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