SMTL ID : 6f7w.1

Crystal structure of dimethylated RSL - cucurbit[7]uril complex, C2221 Form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

homo-trimer

Ligands

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

QQ7.1: 4 residues within 4Å: Chain A: K.34, G.35, W.36, Y.37 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.35, A:W.36, A:W.36 QQ7.5: 5 residues within 4Å: Chain B: K.34, G.35, W.36, Y.37 Ligands: NA.8 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.32, B:G.35 QQ7.9: 4 residues within 4Å: Chain C: K.34, G.35, W.36, Y.37 3 PLIP interactions: 3 interactions with chain C Water bridges: C:D.32, C:G.35, C:W.36

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.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: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:W.36, A:R.62, A:A.85, A:Y.86 GOL.3: 7 residues within 4Å: Chain A: R.17, E.28, A.40, F.41, I.61, W.76, W.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.17, A:A.40, A:F.41 GOL.4: 7 residues within 4Å: Chain A: S.2, Q.4, A.21, N.22, N.23, G.24, D.46 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.2, A:G.24 Water bridges: A:S.2, A:V.3, A:N.23, A:N.23 GOL.6: 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.62, B:A.85, B:Y.86 GOL.7: 7 residues within 4Å: Chain B: R.17, E.28, A.40, F.41, I.61, W.76, W.81 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.17, B:A.40, B:F.41 GOL.10: 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: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.62, C:A.85, C:Y.86, B:W.36 GOL.11: 7 residues within 4Å: Chain C: R.17, E.28, A.40, F.41, I.61, W.76, W.81 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.17, C:A.40, C:F.41 GOL.12: 6 residues within 4Å: Chain A: T.69 Chain C: S.1, S.2, V.3, N.22, N.23 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.22, C:N.23 Water bridges: C:S.2, C:A.21, C:N.22, C:G.24

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

NA.8: 1 residues within 4Å: Ligands: QQ7.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guagnini, F. et al., Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Angew. Chem. Int. Ed. Engl. (2018)

Release Date

2018-05-30

Peptides

Fucose-binding lectin protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fucose-binding lectin protein

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