SMTL ID : 5al0.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: K.70, E.72, H.90, E.92 Chain B: K.35, W.41 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.72, A:E.92, B:W.41 Water bridges: A:K.70, A:K.70, B:K.35, B:K.35 Salt bridges: A:K.70, A:H.90, B:K.35 SO4.4: 6 residues within 4Å: Chain A: K.35, W.41 Chain B: K.70, E.72, H.90, E.92 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:W.41 Water bridges: A:K.35, A:K.70, B:K.70, B:K.70 Salt bridges: A:K.35, B:K.70, B:H.90 SO4.6: 6 residues within 4Å: Chain C: K.70, E.72, H.90, E.92 Chain D: K.35, W.41 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:E.72, C:E.92, D:W.41 Water bridges: C:K.70, C:K.70, D:K.35, D:K.35 Salt bridges: C:K.70, C:H.90, D:K.35 SO4.9: 6 residues within 4Å: Chain C: K.35, W.41 Chain D: K.70, E.72, H.90, E.92 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain C Water bridges: D:K.70, D:K.70, C:K.35, C:K.70 Salt bridges: D:K.70, D:H.90, C:K.35 Hydrogen bonds: C:W.41

4 x R3S: RESVERATROL-3-O-SULFATE(Non-covalent)

R3S.2: 20 residues within 4Å: Chain A: M.13, K.15, L.17, T.106, A.108, L.110, S.117, T.118, T.119, V.121 Chain C: M.13, K.15, L.17, T.106, A.108, L.110, S.117, T.118, T.119 Ligands: R3S.7 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.17, C:L.110, A:L.17, A:A.108, A:L.110 Water bridges: C:K.15, C:K.15, C:S.117, A:T.106 Salt bridges: C:K.15 R3S.5: 20 residues within 4Å: Chain B: M.13, K.15, L.17, T.106, A.108, L.110, S.117, T.118, T.119, V.121 Chain D: M.13, K.15, L.17, T.106, A.108, L.110, S.117, T.118, T.119 Ligands: R3S.10 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:L.17, D:T.119, B:L.110, B:L.110 Hydrogen bonds: D:S.117, B:K.15, B:T.106, B:T.106, B:S.117 Salt bridges: D:K.15 R3S.7: 20 residues within 4Å: Chain A: M.13, K.15, L.17, T.106, A.108, L.110, S.117, T.118, T.119 Chain C: M.13, K.15, L.17, T.106, A.108, L.110, S.117, T.118, T.119, V.121 Ligands: R3S.2 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.17, A:L.110, C:L.17, C:A.108, C:L.110 Water bridges: A:K.15, A:K.15, A:S.117, C:T.106 Salt bridges: A:K.15 R3S.10: 20 residues within 4Å: Chain B: M.13, K.15, L.17, T.106, A.108, L.110, S.117, T.118, T.119 Chain D: M.13, K.15, L.17, T.106, A.108, L.110, S.117, T.118, T.119, V.121 Ligands: R3S.5 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:L.17, B:T.119, D:L.110, D:L.110 Hydrogen bonds: B:S.117, D:K.15, D:T.106, D:T.106, D:S.117 Salt bridges: B:K.15

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

DMS.3: 4 residues within 4Å: Chain A: R.103, V.122 Chain B: Y.114 Chain C: R.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.103 Water bridges: A:S.100 DMS.8: 4 residues within 4Å: Chain A: R.21 Chain C: R.103, V.122 Chain D: Y.114 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.103 Water bridges: C:S.100

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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