SMTL ID : 5aks.1

Transthyretin binding heterogeneity and anti-amyloidogenic activity of natural polyphenols and their metabolites: resveratrol-3-O- glucuronide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.70, E.72, H.90, E.92 Chain B: W.41 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.72 Water bridges: A:K.70, A:K.70, A:K.70, A:K.70 Salt bridges: A:K.70, A:H.90, B:K.35 SO4.3: 5 residues within 4Å: Chain A: K.35, W.41 Chain B: K.70, E.72, H.90 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Water bridges: B:K.70, B:K.70, B:E.72, B:E.72, A:K.70 Salt bridges: B:K.70, B:H.90, A:K.35 Hydrogen bonds: A:W.41 SO4.6: 5 residues within 4Å: Chain C: K.70, E.72, H.90, E.92 Chain D: W.41 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain C Salt bridges: D:K.35, C:K.70, C:H.90 Hydrogen bonds: C:E.72 Water bridges: C:K.70, C:K.70, C:K.70, C:K.70 SO4.8: 5 residues within 4Å: Chain C: K.35, W.41 Chain D: K.70, E.72, H.90 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C Water bridges: D:K.70, D:K.70, D:E.72, D:E.72, C:K.70 Salt bridges: D:K.70, D:H.90, C:K.35 Hydrogen bonds: C:W.41

4 x R3X: Resveratrol-3-O-glucuronide(Non-covalent)

R3X.2: 14 residues within 4Å: Chain A: K.15, L.17, A.108, L.110, S.117, T.119 Chain C: K.15, L.17, T.106, L.110, S.117, T.119, V.121 Ligands: R3X.7 17 PLIP interactions: 9 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:K.15, C:L.17, C:L.110, A:A.108, A:L.110 Hydrogen bonds: C:T.106, C:S.117, A:K.15, A:S.117 Water bridges: C:K.15, C:E.54, C:E.54, C:T.106, A:K.15, A:S.52 Salt bridges: A:K.15, A:K.15 R3X.4: 16 residues within 4Å: Chain B: M.13, K.15, L.17, E.54, T.106, A.108, L.110, S.117, T.119 Chain D: K.15, L.17, T.106, L.110, S.117, T.119 Ligands: R3X.9 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:A.108, B:L.110, D:L.17, D:L.110 Hydrogen bonds: B:E.54, B:S.117, D:S.117 Water bridges: D:K.15, D:K.15, D:K.15 Salt bridges: D:K.15 R3X.7: 14 residues within 4Å: Chain A: K.15, L.17, T.106, L.110, S.117, T.119, V.121 Chain C: K.15, L.17, A.108, L.110, S.117, T.119 Ligands: R3X.2 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:A.108, C:L.110, A:K.15, A:L.17, A:L.110 Hydrogen bonds: C:K.15, C:S.117, A:T.106, A:S.117 Water bridges: C:K.15, C:S.52, A:K.15, A:E.54, A:E.54, A:T.106 Salt bridges: C:K.15, C:K.15 R3X.9: 16 residues within 4Å: Chain B: K.15, L.17, T.106, L.110, S.117, T.119 Chain D: M.13, K.15, L.17, E.54, T.106, A.108, L.110, S.117, T.119 Ligands: R3X.4 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:L.17, B:L.110, D:A.108, D:L.110 Hydrogen bonds: B:S.117, D:E.54, D:S.117 Water bridges: B:K.15, B:K.15, B:K.15 Salt bridges: B:K.15

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 3 residues within 4Å: Chain A: R.103, V.122 Chain B: Y.114 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.103 DMS.10: 3 residues within 4Å: Chain C: R.103, V.122 Chain D: Y.114 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Florio, P. et al., Transthyretin Binding Heterogeneity and Anti-Amyloidogenic Activity of Natural Polyphenols and Their Metabolites. J.Biol.Chem. (2015)

Release Date

2015-10-21

Peptides

TRANSTHYRETIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

TRANSTHYRETIN

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