SMTL ID : 8w45.1

X-ray crystal structure of V30M-TTR in complex with pinostilbene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-tetramer

Ligands

4 x 8KZ: 3-[(E)-2-(4-hydroxyphenyl)ethenyl]-5-methoxy-phenol(Non-covalent)

8KZ.1: 16 residues within 4Å: Chain A: K.47, L.49, T.138, A.140, L.142, S.149, T.151 Chain C: M.45, K.47, L.49, T.138, A.140, L.142, S.149, T.151 Ligands: 8KZ.5 8 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:L.49, A:A.140, A:L.142, A:L.142, C:K.47 Hydrogen bonds: C:S.149 Water bridges: D:S.149, B:S.149 8KZ.4: 16 residues within 4Å: Chain B: K.47, L.49, T.138, A.140, L.142, S.149, T.151 Chain D: K.47, L.49, T.138, A.140, L.142, S.149, T.151, V.153 Ligands: 8KZ.8 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:L.142, B:K.47, B:L.49, B:L.142 Hydrogen bonds: D:S.149 8KZ.5: 16 residues within 4Å: Chain A: M.45, K.47, L.49, T.138, A.140, L.142, S.149, T.151 Chain C: K.47, L.49, T.138, A.140, L.142, S.149, T.151 Ligands: 8KZ.1 8 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:K.47, C:L.49, C:A.140, C:L.142, C:L.142 Hydrogen bonds: A:S.149 Water bridges: D:S.149, B:S.149 8KZ.8: 16 residues within 4Å: Chain B: K.47, L.49, T.138, A.140, L.142, S.149, T.151, V.153 Chain D: K.47, L.49, T.138, A.140, L.142, S.149, T.151 Ligands: 8KZ.4 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:K.47, D:L.49, D:L.142, B:L.142 Hydrogen bonds: B:S.149

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

NA.2: 2 residues within 4Å: Chain A: D.131, S.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.131 NA.3: 2 residues within 4Å: Chain B: D.131, S.132 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.132, B:S.132 NA.6: 2 residues within 4Å: Chain C: D.131, S.132 No protein-ligand interaction detected (PLIP) NA.7: 2 residues within 4Å: Chain D: D.131, S.132 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.131, D:S.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokoyama, T. et al., Resveratrol Derivatives Inhibit Transthyretin Fibrillization: Structural Insights into the Interactions between Resveratrol Derivatives and Transthyretin. J.Med.Chem. (2023)

Release Date

2023-11-22

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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