SMTL ID : 4qxv.1

CRYSTAL STRUCTURE of HUMAN TRANSTHYRETIN IN COMPLEX WITH LUTEOLIN AT 1.1 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

homo-tetramer

Ligands

4 x LU2: 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one(Non-covalent)

LU2.1: 18 residues within 4Å: Chain A: K.15, L.17, T.106, A.108, A.109, L.110, S.117, T.118, T.119 Chain C: K.15, L.17, A.108, A.109, L.110, S.117, T.118, T.119 Ligands: LU2.7 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:L.17, A:A.108, A:L.110, C:K.15, C:A.108 Hydrogen bonds: A:S.117, A:T.119, A:T.119, C:A.108, C:T.119 Water bridges: A:A.109, C:K.15 LU2.5: 18 residues within 4Å: Chain B: K.15, L.17, T.106, A.108, A.109, L.110, S.117, T.118, T.119 Chain D: K.15, L.17, A.108, A.109, L.110, S.117, T.118, T.119 Ligands: LU2.11 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:L.17, B:A.108, B:L.110, D:K.15, D:L.17 Hydrogen bonds: B:S.117, B:T.119, D:A.108 LU2.7: 18 residues within 4Å: Chain A: K.15, L.17, A.108, A.109, L.110, S.117, T.118, T.119 Chain C: K.15, L.17, T.106, A.108, A.109, L.110, S.117, T.118, T.119 Ligands: LU2.1 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:K.15, A:A.108, C:L.17, C:A.108, C:L.110 Hydrogen bonds: A:A.108, A:T.119, C:S.117, C:T.119, C:T.119 Water bridges: A:K.15, C:A.109 LU2.11: 18 residues within 4Å: Chain B: K.15, L.17, A.108, A.109, L.110, S.117, T.118, T.119 Chain D: K.15, L.17, T.106, A.108, A.109, L.110, S.117, T.118, T.119 Ligands: LU2.5 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:K.15, B:L.17, D:L.17, D:A.108, D:L.110 Hydrogen bonds: B:A.108, D:S.117, D:T.119

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: S.85, P.86, F.87, Y.114 Chain B: N.98, Y.105, V.122 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.98 Water bridges: A:S.85 GOL.3: 4 residues within 4Å: Chain A: R.103, V.122, T.123, N.124 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:Y.114, A:R.103, A:N.124 Hydrogen bonds: A:R.103, A:N.124 GOL.6: 14 residues within 4Å: Chain A: S.117 Chain B: A.19, L.110, L.111, S.112, S.115, Y.116, S.117 Chain C: A.19, L.110, S.112, S.115, S.117 Chain D: S.117 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.112, B:S.112, B:S.115, B:Y.116 Water bridges: C:S.117, C:S.117 GOL.8: 7 residues within 4Å: Chain C: S.85, P.86, F.87, Y.114 Chain D: N.98, Y.105, V.122 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:S.85 Hydrogen bonds: D:N.98 GOL.9: 4 residues within 4Å: Chain C: R.103, V.122, T.123, N.124 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.103, C:N.124 Water bridges: C:R.103, C:N.124, D:Y.114 GOL.12: 14 residues within 4Å: Chain A: A.19, L.110, S.112, S.115, S.117 Chain B: S.117 Chain C: S.117 Chain D: A.19, L.110, L.111, S.112, S.115, Y.116, S.117 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:S.112, D:S.112, D:S.115, D:Y.116 Water bridges: A:S.117, A:S.117

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

NA.4: 2 residues within 4Å: Chain A: D.99, S.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.99 Water bridges: A:D.99 NA.10: 2 residues within 4Å: Chain C: D.99, S.100 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.99 Water bridges: C:D.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iakovleva, I. et al., The flavonoid luteolin, but not luteolin-7-o-glucoside, prevents a transthyretin mediated toxic response. Plos One (2015)

Release Date

2015-06-03

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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