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

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

Coordinates

PDB Format

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

QJB.1: 12 residues within 4Å: Chain A: R.15, E.26, Y.35, G.37, A.38, F.39, V.57, I.59, W.74, D.77, G.78, W.79 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.38, A:V.57, A:I.59, A:W.74 Hydrogen bonds: A:A.38, A:F.39 Water bridges: A:R.15, A:R.15, A:R.15 Salt bridges: A:R.15 QJB.2: 9 residues within 4Å: Chain A: R.60, E.71, G.82, A.83, Y.84 Chain B: P.12, I.14, Y.29, W.34 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.14, B:Y.29, A:A.83 Hydrogen bonds: A:R.60, A:A.83, A:Y.84 Water bridges: A:A.83 Salt bridges: A:R.60 QJB.3: 10 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:V.57, B:I.59, B:W.74 Hydrogen bonds: B:Y.35, 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: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.51, B:A.83, C:I.14, C:Y.29 Hydrogen bonds: B:A.83, B:Y.84 Salt bridges: B:R.60 QJB.5: 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:A.38, C:F.39 Water bridges: C:R.15 Salt bridges: C:R.15 QJB.6: 9 residues within 4Å: Chain A: P.12, I.14, Y.29, W.34 Chain C: R.60, E.71, G.82, A.83, Y.84 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.83, A:I.14, A:Y.29 Hydrogen bonds: C:A.83, C:Y.84 Salt bridges: C:R.60

Links

RCSB   PDBe   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
A

B
B

C
C

bacterial lectin from Burkholderia ambifaria

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