SMTL ID : 6su0.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-9-mer

Ligands

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

NA.1: 1 residues within 4Å: Ligands: QQ7.12 No protein-ligand interaction detected (PLIP) NA.4: 1 residues within 4Å: Ligands: QQ7.16 No protein-ligand interaction detected (PLIP)

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

MFU.2: 20 residues within 4Å: Chain A: W.52, R.61, E.72, Y.81, A.84, Y.85 Chain C: P.13, I.15, W.30, W.35 Chain G: R.16, E.27, Y.36, G.38, A.39, F.40, I.58, I.60, W.75, W.80 15 PLIP interactions: 8 interactions with chain G, 3 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: G:I.58, G:I.60, G:W.75, C:P.13, C:I.15, C:W.30, A:W.52 Hydrogen bonds: G:E.27, G:A.39, G:F.40, G:W.80, A:E.72, A:Y.85 Salt bridges: G:R.16, A:R.61 MFU.3: 18 residues within 4Å: Chain A: I.15, W.30, W.35 Chain B: R.61, E.72, C.74, Y.81, G.83, A.84, Y.85 Chain H: R.16, E.27, Y.36, A.39, I.58, I.60, W.75, W.80 16 PLIP interactions: 9 interactions with chain H, 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: H:I.58, H:I.60, H:W.75, A:I.15, A:W.30 Hydrogen bonds: H:E.27, H:E.27, H:A.39, H:F.40, H:W.80, B:R.61, B:E.72, B:A.84, A:W.35 Salt bridges: H:R.16, B:R.61 MFU.5: 18 residues within 4Å: Chain C: R.16, E.27, G.38, A.39, I.58, I.60, W.75, W.80 Chain G: W.52, R.61, E.72, Y.81, G.83, A.84 Chain I: P.13, I.15, W.30, W.35 7 PLIP interactions: 1 interactions with chain I, 3 interactions with chain C, 3 interactions with chain G Hydrogen bonds: I:W.35, C:E.27, C:W.75, G:R.61, G:R.61 Salt bridges: C:R.16, G:R.61 MFU.7: 8 residues within 4Å: Chain D: R.16, E.27, G.38, A.39, F.40, I.60, W.75, W.80 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.60, D:W.75 Hydrogen bonds: D:R.16, D:E.27, D:A.39, D:F.40 Salt bridges: D:R.16 MFU.14: 20 residues within 4Å: Chain A: W.9, R.16, E.27, Y.36, G.38, A.39, I.60, W.75, W.80 Chain G: P.13, I.15, W.30, W.35 Chain H: W.52, R.61, E.72, Y.81, G.83, A.84, Y.85 14 PLIP interactions: 6 interactions with chain H, 4 interactions with chain A, 4 interactions with chain G Hydrophobic interactions: H:W.52, A:W.9, A:I.60, A:W.75, G:P.13, G:I.15, G:W.30 Hydrogen bonds: H:R.61, H:E.72, H:E.72, H:A.84, G:W.35 Salt bridges: H:R.61, A:R.16 MFU.17: 18 residues within 4Å: Chain B: W.9, R.16, E.27, G.38, A.39, I.60, W.75, W.80 Chain H: P.13, I.15, W.30, W.35 Chain I: R.61, E.72, Y.81, G.83, A.84, Y.85 13 PLIP interactions: 7 interactions with chain B, 3 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: B:W.9, B:I.60, B:W.75, H:P.13, H:I.15, H:W.30 Hydrogen bonds: B:E.27, B:W.80, I:A.84, I:A.84 Water bridges: B:Y.36 Salt bridges: B:R.16, I:R.61 MFU.18: 21 residues within 4Å: Chain B: P.13, I.15, W.30, W.35 Chain C: W.52, R.61, E.72, Y.81, G.83, A.84, Y.85 Chain I: R.16, Y.18, E.27, Y.36, G.38, A.39, I.58, I.60, W.75, W.80 11 PLIP interactions: 3 interactions with chain B, 4 interactions with chain I, 4 interactions with chain C Hydrophobic interactions: B:I.15, B:W.30, I:I.58, I:I.60, I:W.75, C:W.52 Hydrogen bonds: B:W.35, C:E.72, C:A.84 Salt bridges: I:R.16, C:R.61

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

QQ7.6: 4 residues within 4Å: Chain D: D.31, K.33, G.34, Y.36 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.34 QQ7.8: 4 residues within 4Å: Chain E: D.31, K.33, G.34, Y.36 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.34 QQ7.9: 4 residues within 4Å: Chain F: D.31, K.33, G.34, Y.36 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.34 QQ7.10: 8 residues within 4Å: Chain A: D.76, K.78, G.79, Y.81 Chain G: D.31, K.33, G.34, Y.36 No protein-ligand interaction detected (PLIP) QQ7.11: 8 residues within 4Å: Chain C: D.31, K.33, G.34, Y.36 Chain G: D.76, K.78, G.79, Y.81 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.79, G:G.79 QQ7.12: 9 residues within 4Å: Chain A: D.31, K.33, G.34, Y.36 Chain H: D.76, K.78, G.79, Y.81 Ligands: NA.1 No protein-ligand interaction detected (PLIP) QQ7.13: 8 residues within 4Å: Chain B: D.76, K.78, G.79, Y.81 Chain H: D.31, K.33, G.34, Y.36 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain B Water bridges: H:G.34, H:G.34, B:D.76 QQ7.15: 8 residues within 4Å: Chain B: D.31, K.33, G.34, Y.36 Chain I: D.76, K.78, G.79, Y.81 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.79 QQ7.16: 9 residues within 4Å: Chain C: D.76, K.78, G.79, Y.81 Chain I: D.31, K.33, G.34, Y.36 Ligands: NA.4 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:G.34, I:G.34

Links

RCSB   PDBe   PDBe-KB   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: ABCDEFGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
I

E
J

F
K

G
M

H
N

I
O

Fucose-binding lectin protein

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