SMTL ID : 8ig1.1

Crystal structure of wild-type transthyretin in complex with rafoxanide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

4 x OX9: ~{N}-[3-chloranyl-4-(4-chloranylphenoxy)phenyl]-3,5-bis(iodanyl)-2-oxidanyl-benzamide(Non-covalent)

OX9.1: 15 residues within 4Å: Chain A: K.47, L.49, P.56, S.84, T.138, A.140, T.151, A.152, V.153 Chain C: K.47, L.49, T.138, V.153, T.155 Ligands: OX9.5 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:K.47, A:P.56, A:T.138, A:A.140, A:V.153, C:L.49, C:V.153, C:T.155 Halogen bonds: A:T.151 Hydrogen bonds: C:K.47 OX9.3: 15 residues within 4Å: Chain B: K.47, L.49, T.138, V.153, T.155 Chain D: K.47, L.49, P.56, S.84, T.138, A.140, T.151, A.152, V.153 Ligands: OX9.7 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:L.49, B:V.153, B:T.155, D:L.49, D:T.138, D:A.140, D:V.153 Hydrogen bonds: B:K.47, B:T.138 pi-Cation interactions: D:K.47 Halogen bonds: D:T.151 OX9.5: 15 residues within 4Å: Chain A: K.47, L.49, T.138, V.153, T.155 Chain C: K.47, L.49, P.56, S.84, T.138, A.140, T.151, A.152, V.153 Ligands: OX9.1 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:L.49, A:V.153, A:T.155, C:K.47, C:P.56, C:T.138, C:A.140, C:V.153 Hydrogen bonds: A:K.47 Halogen bonds: C:T.151 OX9.7: 15 residues within 4Å: Chain B: K.47, L.49, P.56, S.84, T.138, A.140, T.151, A.152, V.153 Chain D: K.47, L.49, T.138, V.153, T.155 Ligands: OX9.3 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:L.49, B:T.138, B:A.140, B:V.153, D:L.49, D:V.153, D:T.155 pi-Cation interactions: B:K.47 Halogen bonds: B:T.151 Hydrogen bonds: D:K.47, D:T.138

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:E.98 NA.4: 1 residues within 4Å: Chain B: D.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.131 NA.6: 1 residues within 4Å: Chain C: D.131 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.98 NA.8: 1 residues within 4Å: Chain D: D.131 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., Rafoxanide, a salicylanilide anthelmintic, interacts with human plasma protein transthyretin. Febs J. (2023)

Release Date

2023-08-16

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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