SMTL ID : 6su0.1 (1 other biounit)

Crystal structure of dimethylated RSLex in complex with cucurbit[7]uril

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-hexamer

Ligands

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

NA.1: 1 residues within 4Å: Ligands: QQ7.16 No protein-ligand interaction detected (PLIP) NA.7: 1 residues within 4Å: Ligands: QQ7.15 No protein-ligand interaction detected (PLIP) NA.8: 1 residues within 4Å: Ligands: QQ7.10 No protein-ligand interaction detected (PLIP) NA.9: 1 residues within 4Å: Ligands: QQ7.10 No protein-ligand interaction detected (PLIP)

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

QQ7.2: 8 residues within 4Å: Chain A: D.31, K.33, G.34, Y.36 Chain D: D.76, K.78, G.79, Y.81 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.79, A:G.34 QQ7.5: 8 residues within 4Å: Chain B: D.31, K.33, G.34, Y.36 Chain E: D.76, K.78, G.79, Y.81 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.79, E:G.79 Water bridges: E:H.59 QQ7.10: 10 residues within 4Å: Chain C: D.31, K.33, G.34, Y.36 Chain F: D.76, K.78, G.79, Y.81 Ligands: NA.8, NA.9 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.79 Water bridges: F:G.79 QQ7.13: 8 residues within 4Å: Chain B: D.76, K.78, G.79, Y.81 Chain D: D.31, K.33, G.34, Y.36 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.34, B:G.79 Water bridges: D:D.31, D:W.35 QQ7.15: 9 residues within 4Å: Chain C: D.76, K.78, G.79, Y.81 Chain E: D.31, K.33, G.34, Y.36 Ligands: NA.7 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.34 Water bridges: E:D.31, E:W.35 QQ7.16: 9 residues within 4Å: Chain A: D.76, K.78, G.79, Y.81 Chain F: D.31, K.33, G.34, Y.36 Ligands: NA.1 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.34, F:G.34, A:G.79 Water bridges: F:W.35

6 x MFU: methyl alpha-L-fucopyranoside(Non-covalent)

MFU.3: 21 residues within 4Å: Chain A: R.16, E.27, G.38, A.39, F.40, I.58, I.60, W.75, W.80 Chain D: W.52, R.61, E.72, C.74, Y.81, G.83, A.84, Y.85 Chain F: P.13, I.15, W.30, W.35 13 PLIP interactions: 2 interactions with chain F, 6 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: F:P.13, F:I.15, D:W.52, A:I.58, A:I.60 Hydrogen bonds: D:Y.81, D:A.84, D:A.84, D:Y.85, A:E.27, A:E.27 Salt bridges: D:R.61, A:R.16 MFU.4: 20 residues within 4Å: Chain A: R.61, E.72, Y.81, G.83, A.84, Y.85 Chain C: P.13, I.15, W.30, W.35 Chain F: W.9, R.16, E.27, C.29, G.38, A.39, I.58, I.60, W.75, W.80 15 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A, 7 interactions with chain F Hydrophobic interactions: C:P.13, C:I.15, C:W.30, F:W.9, F:I.58, F:I.60 Hydrogen bonds: C:W.35, A:E.72, A:Y.81, A:A.84, F:E.27, F:E.27, F:W.80 Salt bridges: A:R.61, F:R.16 MFU.6: 19 residues within 4Å: Chain B: R.16, E.27, G.38, A.39, F.40, I.58, I.60, W.75, W.80 Chain D: I.15, W.30, W.35 Chain E: W.52, R.61, E.72, Y.81, G.83, A.84, Y.85 16 PLIP interactions: 7 interactions with chain B, 6 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: B:I.58, B:I.60, B:W.75, E:W.52, D:I.15, D:W.30 Hydrogen bonds: B:E.27, B:A.39, B:W.75, E:R.61, E:R.61, E:A.84, D:W.35 Salt bridges: B:R.16, E:R.61 Water bridges: E:Y.81 MFU.11: 19 residues within 4Å: Chain C: R.16, E.27, G.38, A.39, F.40, I.60, W.75, W.80 Chain E: P.13, I.15, W.30, W.35 Chain F: W.52, R.61, E.72, Y.81, G.83, A.84, Y.85 18 PLIP interactions: 8 interactions with chain C, 6 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: C:I.60, C:W.75, F:W.52, E:P.13, E:I.15, E:W.30 Hydrogen bonds: C:R.16, C:E.27, C:E.27, C:A.39, C:A.39, F:R.61, F:R.61, F:A.84, F:Y.85, E:W.35 Salt bridges: C:R.16, F:R.61 MFU.12: 21 residues within 4Å: Chain B: P.13, I.15, W.30, W.35 Chain C: W.52, R.61, E.72, C.74, G.83, A.84, Y.85 Chain E: R.16, E.27, Y.36, G.38, A.39, F.40, I.58, I.60, W.75, W.80 15 PLIP interactions: 4 interactions with chain C, 8 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: C:W.52, E:I.58, E:I.60, B:I.15, B:W.30 Hydrogen bonds: C:R.61, C:Y.85, E:E.27, E:A.39, E:A.39, E:F.40, E:W.80, B:W.35 Salt bridges: C:R.61, E:R.16 MFU.14: 19 residues within 4Å: Chain A: P.13, I.15, W.30, W.35 Chain B: W.52, R.61, E.72, Y.81, G.83, A.84, Y.85 Chain D: R.16, E.27, G.38, A.39, F.40, I.60, W.75, W.80 14 PLIP interactions: 5 interactions with chain B, 7 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: B:W.52, D:I.60, D:W.75, A:I.15, A:W.30 Hydrogen bonds: B:E.72, B:E.72, B:Y.85, D:R.16, D:R.16, D:A.39, D:A.39 Salt bridges: B:R.61, D:R.16

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Guagnini, F. et al., Engineered assembly of a protein-cucurbituril biohybrid. Chem.Commun.(Camb.) (2020)

Release Date

2020-02-19

Peptides

Fucose-binding lectin protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
I

E
J

F
K

Fucose-binding lectin protein

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