SMTL ID : 4der.1

Crystal Structure of the Wild Type TTR Binding Apigenin (TTRwt:API)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x AGI: 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one(Non-covalent)

AGI.1: 8 residues within 4Å: Chain A: K.6, A.99, L.101 Chain C: K.6, T.97, A.99, L.101 Ligands: AGI.4 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:K.6, C:A.99, C:L.101, A:K.6, A:L.101 Water bridges: C:K.6, C:K.6, C:L.101, A:L.101 Hydrogen bonds: A:K.6 pi-Cation interactions: A:K.6 AGI.3: 12 residues within 4Å: Chain B: K.6, L.8, T.97, A.99, L.101, S.108 Chain D: K.6, L.8, A.99, L.101, S.108 Ligands: AGI.6 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: D:K.6, D:L.8, D:L.101, B:K.6, B:L.101 Hydrogen bonds: D:K.6, D:S.108, B:K.6, B:S.108, B:S.108 Water bridges: D:L.101, B:K.6, B:L.101 AGI.4: 8 residues within 4Å: Chain A: K.6, T.97, A.99, L.101 Chain C: K.6, A.99, L.101 Ligands: AGI.1 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:K.6, C:L.101, A:K.6, A:A.99, A:L.101 Hydrogen bonds: C:K.6 Water bridges: C:L.101, A:K.6, A:K.6, A:L.101 pi-Cation interactions: C:K.6 AGI.6: 12 residues within 4Å: Chain B: K.6, L.8, A.99, L.101, S.108 Chain D: K.6, L.8, T.97, A.99, L.101, S.108 Ligands: AGI.3 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:K.6, B:L.8, B:L.101, D:K.6, D:L.101 Hydrogen bonds: B:K.6, B:S.108, D:K.6, D:S.108, D:S.108 Water bridges: B:L.101, D:K.6, D:L.101

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: E.57, D.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.57 GOL.5: 2 residues within 4Å: Chain C: E.57, D.90 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trivella, D.B. et al., Flavonoid interactions with human transthyretin: Combined structural and thermodynamic analysis. J.Struct.Biol. (2012)

Release Date

2012-11-21

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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