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

Highly cationic RSL-R8 in complex with sulfonato-calix[8]arene

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-trimer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: R.62, E.73, G.84, A.85, Y.86 Chain B: I.16, W.31, W.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.62, A:A.85, A:Y.86 GOL.2: 6 residues within 4Å: Chain A: R.17, E.28, A.40, F.41, W.76, W.81 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.17, A:E.28, A:A.40, A:F.41, A:W.81 Water bridges: A:D.32 GOL.5: 1 residues within 4Å: Ligands: EVB.4 No protein-ligand interaction detected (PLIP) GOL.6: 8 residues within 4Å: Chain B: R.62, E.73, G.84, A.85, Y.86 Chain C: I.16, W.31, W.36 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.62, B:A.85, B:Y.86 GOL.7: 6 residues within 4Å: Chain B: R.17, E.28, A.40, F.41, W.76, W.81 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.17, B:E.28, B:A.40, B:F.41, B:W.81 Water bridges: B:D.32 GOL.10: 1 residues within 4Å: Ligands: EVB.9 No protein-ligand interaction detected (PLIP) GOL.11: 8 residues within 4Å: Chain A: I.16, W.31, W.36 Chain C: R.62, E.73, G.84, A.85, Y.86 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.62, C:A.85, C:Y.86 GOL.12: 6 residues within 4Å: Chain C: R.17, E.28, A.40, F.41, W.76, W.81 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.17, C:E.28, C:A.40, C:F.41, C:W.81 Water bridges: C:D.32 GOL.15: 1 residues within 4Å: Ligands: EVB.14 No protein-ligand interaction detected (PLIP)

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

SO4.3: 4 residues within 4Å: Chain A: A.40, W.76, G.80, W.81 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.81, A:W.81 Water bridges: A:R.43, A:R.43, A:R.43 SO4.8: 4 residues within 4Å: Chain B: A.40, W.76, G.80, W.81 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.81, B:W.81 Water bridges: B:R.43, B:R.43, B:R.43 SO4.13: 4 residues within 4Å: Chain C: A.40, W.76, G.80, W.81 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:W.81, C:W.81 Water bridges: C:R.43, C:R.43, C:R.43

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

EVB.4: 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 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.44, A:W.74 Hydrogen bonds: A:N.23, A:R.25, A:R.25, A:T.67, A:G.68, A:T.69, A:T.72 Water bridges: A:R.25, A:R.43, A:R.43, A:T.69, A:T.69, A:T.72 Salt bridges: A:R.43, A:R.46, A:R.46 pi-Cation interactions: A:R.43 EVB.9: 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 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:P.44, B:W.74 Hydrogen bonds: B:N.23, B:R.25, B:R.25, B:T.67, B:G.68, B:T.69, B:T.72 Water bridges: B:R.25, B:R.43, B:R.43, B:T.69, B:T.69, B:T.72 Salt bridges: B:R.43, B:R.46, B:R.46 pi-Cation interactions: B:R.43 EVB.14: 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 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:P.44, C:W.74 Hydrogen bonds: C:N.23, C:R.25, C:R.25, C:T.67, C:G.68, C:T.69, C:T.72 Water bridges: C:R.25, C:R.43, C:R.43, C:T.69, C:T.69, C:T.72 Salt bridges: C:R.43, C:R.46, C:R.46 pi-Cation interactions: C:R.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skorek, T. et al., Highly cationic RSL-R8 in complex with sulfonato-calix[8]arene. To Be Published

Release Date

2020-09-30

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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