SMTL ID : 6z5p.1 (1 other biounit)

The RSL-R8 - sulfonato-calix[8]arene complex, P3 form, TRIS-HCl pH 8.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-trimer

Ligands

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

EVB.1: 16 residues within 4Å: Chain A: N.23, G.24, R.25, N.42, R.43, P.44, G.45, R.46, T.67, G.68, T.69, T.70, T.72, W.74, R.83 Ligands: GOL.5 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:P.44, A:W.74, A:W.74 Hydrogen bonds: A:N.23, A:R.25, A:R.25, A:R.25, A:G.45, A:G.68 Water bridges: A:R.25, A:N.42, A:R.43, A:R.46, A:R.46, A:T.69, A:T.69, A:T.70, A:T.70, A:T.72, A:T.72, A:R.83 Salt bridges: A:R.43, A:R.46, A:R.46 pi-Cation interactions: A:R.43 EVB.6: 16 residues within 4Å: Chain B: N.23, G.24, R.25, N.42, R.43, P.44, G.45, R.46, T.67, G.68, T.69, T.70, T.72, W.74, R.83 Ligands: GOL.10 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:P.44, B:W.74, B:W.74 Hydrogen bonds: B:N.23, B:R.25, B:R.25, B:R.25, B:G.45, B:G.68 Water bridges: B:R.25, B:N.42, B:R.43, B:R.46, B:R.46, B:T.69, B:T.69, B:T.70, B:T.70, B:T.72, B:T.72, B:R.83 Salt bridges: B:R.43, B:R.46, B:R.46 pi-Cation interactions: B:R.43 EVB.11: 16 residues within 4Å: Chain C: N.23, G.24, R.25, N.42, R.43, P.44, G.45, R.46, T.67, G.68, T.69, T.70, T.72, W.74, R.83 Ligands: GOL.15 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:P.44, C:W.74, C:W.74 Hydrogen bonds: C:N.23, C:R.25, C:R.25, C:R.25, C:G.45, C:G.68 Water bridges: C:R.25, C:N.42, C:R.43, C:R.46, C:R.46, C:T.69, C:T.69, C:T.70, C:T.70, C:T.72, C:T.72, C:R.83 Salt bridges: C:R.43, C:R.46, C:R.46 pi-Cation interactions: C:R.43

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

BDF.2: 9 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:R.62, A:E.73, A:A.85, A:Y.86 BDF.3: 9 residues within 4Å: Chain A: R.17, E.28, Y.37, G.39, A.40, F.41, I.61, W.76, W.81 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.17, A:E.28, A:Y.37, A:Y.37, A:A.40, A:F.41 Water bridges: A:T.38 BDF.7: 9 residues within 4Å: Chain A: I.16, W.31, W.36 Chain B: R.62, E.73, C.75, G.84, A.85, Y.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.62, B:E.73, B:A.85, B:Y.86 BDF.8: 9 residues within 4Å: Chain B: R.17, E.28, Y.37, G.39, A.40, F.41, I.61, W.76, W.81 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.17, B:E.28, B:Y.37, B:Y.37, B:A.40, B:F.41 Water bridges: B:T.38 BDF.12: 9 residues within 4Å: Chain B: 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 BDF.13: 9 residues within 4Å: Chain C: R.17, E.28, Y.37, G.39, A.40, F.41, I.61, W.76, W.81 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.17, C:E.28, C:Y.37, C:Y.37, C:A.40, C:F.41 Water bridges: C:T.38

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: A.40, W.76, G.80, W.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.81 Water bridges: A:R.43, A:R.43, A:R.43 SO4.9: 4 residues within 4Å: Chain B: A.40, W.76, G.80, W.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.81 Water bridges: B:R.43, B:R.43, B:R.43 SO4.14: 4 residues within 4Å: Chain C: A.40, W.76, G.80, W.81 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.81 Water bridges: C:R.43, C:R.43, C:R.43

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 1 residues within 4Å: Ligands: EVB.1 No protein-ligand interaction detected (PLIP) GOL.10: 1 residues within 4Å: Ligands: EVB.6 No protein-ligand interaction detected (PLIP) GOL.15: 1 residues within 4Å: Ligands: EVB.11 No protein-ligand interaction detected (PLIP)

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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