SMTL ID : 6z5m.1

The RSL - sulfonato-calix[8]arene complex, I23 form, Gly-HCl pH 2.2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

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

EVB.1: 11 residues within 4Å: Chain A: G.24, K.25, A.40, N.42, E.43, P.44, W.74, G.80, W.81, T.82, K.83 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:N.42, A:P.44, A:W.74 Hydrogen bonds: A:N.42, A:E.43, A:E.43, A:W.81, A:K.83 Water bridges: A:K.25, A:N.42, A:N.42, A:N.42, A:N.42, A:N.42 Salt bridges: A:K.25, A:K.25, A:K.83 pi-Stacking: A:W.74, A:W.74 EVB.2: 6 residues within 4Å: Chain A: T.12, V.13, D.32, G.33, K.34 Chain C: H.60 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.13, A:K.34 Hydrogen bonds: A:G.33 Water bridges: A:G.33, A:K.34, A:K.34 Salt bridges: A:K.34, C:H.60 EVB.6: 11 residues within 4Å: Chain B: G.24, K.25, A.40, N.42, E.43, P.44, W.74, G.80, W.81, T.82, K.83 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:N.42, B:P.44, B:W.74 Hydrogen bonds: B:N.42, B:E.43, B:E.43, B:W.81, B:K.83 Water bridges: B:K.25, B:N.42, B:N.42, B:N.42, B:N.42, B:N.42 Salt bridges: B:K.25, B:K.25, B:K.83 pi-Stacking: B:W.74, B:W.74 EVB.7: 6 residues within 4Å: Chain A: H.60 Chain B: T.12, V.13, D.32, G.33, K.34 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.13, B:K.34 Hydrogen bonds: B:G.33 Water bridges: B:G.33, B:K.34, B:K.34 Salt bridges: B:K.34, A:H.60 EVB.11: 11 residues within 4Å: Chain C: G.24, K.25, A.40, N.42, E.43, P.44, W.74, G.80, W.81, T.82, K.83 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:N.42, C:P.44, C:W.74 Hydrogen bonds: C:N.42, C:E.43, C:E.43, C:W.81, C:K.83 Water bridges: C:K.25, C:N.42, C:N.42, C:N.42, C:N.42, C:N.42 Salt bridges: C:K.25, C:K.25, C:K.83 pi-Stacking: C:W.74, C:W.74 EVB.12: 6 residues within 4Å: Chain B: H.60 Chain C: T.12, V.13, D.32, G.33, K.34 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.13, C:K.34 Hydrogen bonds: C:G.33 Water bridges: C:G.33, C:K.34, C:K.34 Salt bridges: C:K.34, B:H.60

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: S.2, Q.4, A.21, N.22, N.23, G.24, D.46 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.23, A:G.24, A:D.46, A:D.46 Water bridges: A:S.1, A:S.2, A:V.3 GOL.8: 7 residues within 4Å: Chain B: S.2, Q.4, A.21, N.22, N.23, G.24, D.46 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.23, B:G.24, B:D.46, B:D.46 Water bridges: B:S.1, B:S.2, B:V.3 GOL.13: 7 residues within 4Å: Chain C: S.2, Q.4, A.21, N.22, N.23, G.24, D.46 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.23, C:G.24, C:D.46 Water bridges: C:S.1, C:S.2, C:V.3

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

BDF.4: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.62, A:E.73, A:A.85, A:Y.86 Water bridges: A:T.82, A:T.82 BDF.5: 9 residues within 4Å: Chain A: R.17, E.28, Y.37, G.39, A.40, F.41, I.61, W.76, W.81 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.17, A:E.28, A:Y.37, A:A.40, A:F.41 Water bridges: A:Y.37, A:Y.37, A:T.38 BDF.9: 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.62, B:E.73, B:A.85, B:Y.86 Water bridges: B:T.82, B:T.82 BDF.10: 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.14: 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 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.62, C:E.73, C:A.85, C:Y.86 Water bridges: C:T.82, C:T.82 BDF.15: 9 residues within 4Å: Chain C: R.17, E.28, Y.37, G.39, A.40, F.41, I.61, W.76, W.81 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.17, C:E.28, C:Y.37, C:A.40, C:F.41 Water bridges: C:Y.37, C:Y.37, 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

2021-04-14

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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