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

Crystal structure of dimethylated RSL in complex with cucurbit[7]uril and zinc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-trimer

Ligands

3 x QQ7: cucurbit[7]uril(Non-covalent)

QQ7.1: 4 residues within 4Å: Chain A: K.34, G.35, W.36, Y.37 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.35 QQ7.4: 6 residues within 4Å: Chain B: K.34, G.35, W.36, Y.37 Ligands: NA.5, NA.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.35 QQ7.9: 4 residues within 4Å: Chain C: K.34, G.35, W.36, Y.37 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.35 Water bridges: C:D.32

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: R.62, E.73, C.75, G.84, A.85, Y.86 Chain B: I.16, W.31, W.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.62, A:E.73, A:A.85, A:Y.86 GOL.3: 8 residues within 4Å: Chain A: R.17, E.28, C.30, A.40, F.41, I.61, W.76, W.81 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.17, A:R.17, A:E.28, A:A.40, A:F.41 GOL.6: 9 residues within 4Å: Chain B: R.17, E.28, C.30, G.39, A.40, F.41, I.61, W.76, W.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.17, B:R.17, B:A.40, B:F.41 GOL.7: 9 residues within 4Å: Chain B: R.62, E.73, C.75, G.84, A.85, Y.86 Chain C: I.16, W.31, W.36 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.62, B:E.73, B:A.85, B:Y.86 GOL.10: 9 residues within 4Å: Chain C: W.10, R.17, E.28, C.30, A.40, F.41, I.61, W.76, W.81 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.17, C:R.17, C:E.28, C:A.40, C:F.41 GOL.11: 9 residues within 4Å: Chain A: I.16, W.31, W.36 Chain C: R.62, E.73, C.75, G.84, A.85, Y.86 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.62, C:E.73, C:A.85, C:Y.86

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

NA.5: 2 residues within 4Å: Ligands: QQ7.4, NA.8 No protein-ligand interaction detected (PLIP) NA.8: 2 residues within 4Å: Ligands: QQ7.4, NA.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guagnini, F. et al., Metal-Mediated Protein-Cucurbituril Crystalline Architectures. Cryst.Growth Des. (2020)

Release Date

2020-11-25

Peptides

Fucose-binding lectin protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
F

Fucose-binding lectin protein

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