SMTL ID : 6gl5.1

Crystal Structure of dimethylated RSL - sulfonatocalix[4]arene complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

6 x T3Y: 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid(Non-covalent)

T3Y.1: 5 residues within 4Å: Chain A: S.1, S.2, N.23, D.46 Ligands: T3Y.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.2, A:N.23, A:N.23 Water bridges: A:G.24, A:G.24 T3Y.7: 6 residues within 4Å: Chain B: S.1, S.2, N.22, N.23 Chain C: G.68, T.69 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.2, B:N.23 Water bridges: B:S.2, B:N.23, C:T.69, C:T.69 T3Y.8: 6 residues within 4Å: Chain B: R.29, W.36, Y.37, T.38 Ligands: PEG.11, PEG.12 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain B Water bridges: C:T.87, B:R.29, B:R.29 Hydrophobic interactions: B:Y.37 Hydrogen bonds: B:T.38, B:T.38 Salt bridges: B:R.29 T3Y.13: 4 residues within 4Å: Chain C: W.74, W.81, T.82, K.83 No protein-ligand interaction detected (PLIP) T3Y.14: 6 residues within 4Å: Chain A: D.46, T.67, G.68 Chain C: S.1, S.2 Ligands: T3Y.1 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.46, A:G.68, C:S.2, C:S.2 T3Y.15: 10 residues within 4Å: Chain C: W.10, S.15, R.17, D.32, S.57, A.58, I.59, W.76, G.78 Ligands: GOL.17 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.10, C:I.59 Hydrogen bonds: C:S.15, C:S.15, C:R.17, C:S.57, C:I.59 Water bridges: C:S.15

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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.3: 8 residues within 4Å: Chain A: R.62, E.73, G.84, A.85, Y.86 Chain C: I.16, W.31, W.36 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.62, A:A.85, A:Y.86, C:W.36 GOL.9: 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 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:W.36, B:R.62, B:A.85, B:Y.86 GOL.10: 7 residues within 4Å: Chain B: R.17, E.28, A.40, F.41, I.61, W.76, W.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.17, B:E.28, B:A.40, B:F.41 GOL.16: 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: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:W.36, C:R.62, C:A.85, C:Y.86 GOL.17: 8 residues within 4Å: Chain C: R.17, E.28, A.40, F.41, I.61, W.76, W.81 Ligands: T3Y.15 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.17, C:A.40, C:F.41

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 5 residues within 4Å: Chain A: A.40, F.41, N.42, E.43, W.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.42, A:N.42, A:E.43

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 4 residues within 4Å: Chain A: R.29, W.36, Y.37, T.38 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.29, A:R.29, A:T.38, A:T.38 PEG.11: 1 residues within 4Å: Ligands: T3Y.8 No protein-ligand interaction detected (PLIP) PEG.12: 3 residues within 4Å: Chain B: Y.37, T.38 Ligands: T3Y.8 No protein-ligand interaction detected (PLIP) PEG.19: 4 residues within 4Å: Chain C: K.34, G.35, W.36, Y.37 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Y.37, C:Y.37

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 1 residues within 4Å: Chain A: Y.37 No protein-ligand interaction detected (PLIP)

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

SO4.18: 4 residues within 4Å: Chain C: R.29, W.36, Y.37, T.38 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.38, C:T.38 Salt bridges: C:R.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guagnini, F. et al., Protein Crystallization via Sulfonatocalix[4]arene Dimethylammonium Complexation. To Be Published

Release Date

2019-06-19

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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