SMTL ID : 6z5q.1 (1 other biounit)

The RSL - sulfonato-calix[8]arene complex, P3 form, acetate pH 4.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

homo-trimer

Ligands

3 x EVB: sulfonato-calix[8]arene(Non-covalent)

EVB.1: 11 residues within 4Å: Chain A: W.10, T.12, V.13, S.15, D.32, G.33, K.34, Y.37 Ligands: GOL.2, GOL.3, BDF.5 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.13, A:V.13, A:K.34, A:Y.37 Hydrogen bonds: A:T.12, A:D.32, A:D.32, A:K.34 Water bridges: A:T.12, A:T.12, A:T.12, A:T.12, A:R.17, A:K.34, A:K.34, A:K.34, A:K.34, A:K.34, A:K.34, A:I.59 Salt bridges: A:K.34, A:K.34 pi-Cation interactions: A:K.34, A:K.34, A:K.34 EVB.6: 11 residues within 4Å: Chain B: W.10, T.12, V.13, S.15, D.32, G.33, K.34, Y.37 Ligands: GOL.7, GOL.8, BDF.10 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:V.13, B:V.13, B:K.34, B:Y.37 Hydrogen bonds: B:T.12, B:D.32, B:D.32, B:K.34 Water bridges: B:T.12, B:T.12, B:T.12, B:T.12, B:R.17, B:K.34, B:K.34, B:K.34, B:K.34, B:K.34, B:K.34, B:I.59 Salt bridges: B:K.34, B:K.34 pi-Cation interactions: B:K.34, B:K.34, B:K.34 EVB.11: 11 residues within 4Å: Chain C: W.10, T.12, V.13, S.15, D.32, G.33, K.34, Y.37 Ligands: GOL.12, GOL.13, BDF.15 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:V.13, C:V.13, C:K.34, C:Y.37 Hydrogen bonds: C:T.12, C:D.32, C:D.32, C:K.34 Water bridges: C:T.12, C:T.12, C:T.12, C:T.12, C:R.17, C:K.34, C:K.34, C:K.34, C:K.34, C:K.34, C:K.34, C:I.59 Salt bridges: C:K.34, C:K.34 pi-Cation interactions: C:K.34, C:K.34, C:K.34

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Ligands: EVB.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.57, A:S.57 GOL.3: 4 residues within 4Å: Chain A: K.34, G.35, Y.37 Ligands: EVB.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.34 GOL.7: 1 residues within 4Å: Ligands: EVB.6 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.57, B:S.57 GOL.8: 4 residues within 4Å: Chain B: K.34, G.35, Y.37 Ligands: EVB.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.34 GOL.12: 1 residues within 4Å: Ligands: EVB.11 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.57, C:S.57 GOL.13: 4 residues within 4Å: Chain C: K.34, G.35, Y.37 Ligands: EVB.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.34

6 x BDF: beta-D-fructopyranose(Non-covalent)

BDF.4: 8 residues within 4Å: Chain A: R.62, E.73, G.84, A.85, Y.86 Chain B: I.16, W.31, W.36 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.62, A:E.73, A:A.85, A:Y.86 Water bridges: A:D.77 BDF.5: 11 residues within 4Å: Chain A: R.17, E.28, C.30, Y.37, G.39, A.40, F.41, I.61, W.76, W.81 Ligands: EVB.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.17, A:E.28, A:Y.37, A:A.40, A:F.41 Water bridges: A:T.38 BDF.9: 8 residues within 4Å: Chain B: R.62, E.73, G.84, A.85, Y.86 Chain C: I.16, W.31, W.36 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.62, B:E.73, B:A.85, B:Y.86 Water bridges: B:D.77 BDF.10: 11 residues within 4Å: Chain B: R.17, E.28, C.30, Y.37, G.39, A.40, F.41, I.61, W.76, W.81 Ligands: EVB.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.17, B:E.28, B:Y.37, B:A.40, B:F.41 Water bridges: B:T.38 BDF.14: 8 residues within 4Å: Chain A: I.16, W.31, W.36 Chain C: R.62, E.73, G.84, A.85, Y.86 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.62, C:E.73, C:A.85, C:Y.86 Water bridges: C:D.77 BDF.15: 11 residues within 4Å: Chain C: R.17, E.28, C.30, Y.37, G.39, A.40, F.41, I.61, W.76, W.81 Ligands: EVB.11 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.17, C:E.28, C:Y.37, C:A.40, C:F.41 Water bridges: C:T.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramberg, K.O. et al., Facile Fabrication of Protein-Macrocycle Frameworks. J.Am.Chem.Soc. (2021)

Release Date

2021-04-07

Peptides

Fucose-binding lectin protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Fucose-binding lectin protein

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