SMTL ID : 8w47.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x P5O: 5-[(~{E})-2-(3-methoxy-4-oxidanyl-phenyl)ethenyl]benzene-1,3-diol(Non-covalent)

P5O.1: 16 residues within 4Å: Chain A: K.47, L.49, A.140, L.142, S.149, T.150, T.151 Chain C: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151 Ligands: P5O.5 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:K.47, A:A.140, A:L.142, C:L.49, C:A.140 Hydrogen bonds: A:K.47, C:K.47 P5O.3: 16 residues within 4Å: Chain B: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151 Chain D: K.47, L.49, A.140, L.142, S.149, T.150, T.151 Ligands: P5O.7 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:A.140, D:L.142, B:L.49, B:A.140, B:T.151 Hydrogen bonds: D:K.47, B:K.47 P5O.5: 16 residues within 4Å: Chain A: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151 Chain C: K.47, L.49, A.140, L.142, S.149, T.150, T.151 Ligands: P5O.1 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:K.47, C:A.140, C:L.142, A:L.49, A:A.140 Hydrogen bonds: C:K.47, A:K.47 P5O.7: 16 residues within 4Å: Chain B: K.47, L.49, A.140, L.142, S.149, T.150, T.151 Chain D: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151 Ligands: P5O.3 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:L.49, D:A.140, D:T.151, B:A.140, B:L.142 Hydrogen bonds: D:K.47, B:K.47

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

NA.2: 1 residues within 4Å: Chain A: D.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.131 NA.4: 2 residues within 4Å: Chain B: D.131, S.132 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.132 NA.6: 1 residues within 4Å: Chain C: D.131 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.131 NA.8: 2 residues within 4Å: Chain D: D.131, S.132 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.131

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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