SMTL ID : 7q9l.1

Transthyretin complexed with (E)-4-(2-(naphthalen-1-yl)vinyl)benzene-1,2-diol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

4 x 9RJ: 4-[(~{E})-2-naphthalen-1-ylethenyl]benzene-1,2-diol(Non-covalent)

9RJ.1: 14 residues within 4Å: Chain A: K.7, L.9, A.100, L.102, S.109, T.111 Chain C: K.7, L.9, A.100, L.102, S.109, T.110, T.111 Ligands: 9RJ.5 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:K.7, C:A.100, C:L.102, C:T.111, A:L.9, A:A.100, A:L.102, A:L.102, A:T.111 9RJ.3: 13 residues within 4Å: Chain B: K.7, L.9, A.100, L.102, S.109, T.111 Chain D: K.7, A.100, L.102, S.109, T.110, T.111 Ligands: 9RJ.7 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:T.111, B:L.9, B:A.100, B:L.102, B:L.102, B:T.111 9RJ.5: 14 residues within 4Å: Chain A: K.7, L.9, A.100, L.102, S.109, T.110, T.111 Chain C: K.7, L.9, A.100, L.102, S.109, T.111 Ligands: 9RJ.1 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.9, C:A.100, C:L.102, C:L.102, C:T.111, A:K.7, A:A.100, A:L.102, A:T.111 9RJ.7: 13 residues within 4Å: Chain B: K.7, A.100, L.102, S.109, T.110, T.111 Chain D: K.7, L.9, A.100, L.102, S.109, T.111 Ligands: 9RJ.3 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.9, D:A.100, D:L.102, D:L.102, D:T.111, B:T.111

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: A.11, L.102, L.103, S.104, S.107, S.109 Chain D: S.104, S.107, Y.108, S.109 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 interactions with chain A Water bridges: B:S.109, B:S.109 Hydrogen bonds: D:Y.108, D:S.109, A:S.109, A:S.109 GOL.6: 10 residues within 4Å: Chain B: S.104, S.107, Y.108, S.109 Chain C: A.11, L.102, L.103, S.104, S.107, S.109 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:Y.108, B:S.109, C:S.109, C:S.109 Water bridges: D:S.109, D:S.109

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

NA.4: 1 residues within 4Å: Chain B: D.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.91 NA.8: 1 residues within 4Å: Chain D: D.91 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Begum, A. et al., Transthyretin Binding Mode Dichotomy of Fluorescent trans -Stilbene Ligands. Acs Chem Neurosci (2023)

Release Date

2022-11-23

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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