SMTL ID : 7dt8.1

Crystal structure of V30M mutated transthyretin in complex with 4-chloro-9-oxo-9H-xanthene-2-carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: E.98, D.131 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.98, A:D.131, A:D.131 CA.3: 3 residues within 4Å: Chain B: E.98, N.130, D.131 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.98, H2O.5 CA.5: 2 residues within 4Å: Chain C: E.98, D.131 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.98, C:D.131, C:D.131 CA.7: 3 residues within 4Å: Chain D: E.98, N.130, D.131 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.98, H2O.13

4 x HH9: 4-chloranyl-9-oxidanylidene-xanthene-2-carboxylic acid(Non-covalent)

HH9.2: 11 residues within 4Å: Chain A: K.47, L.49, T.138, A.140, T.151, V.153 Chain C: K.47, L.49, A.140, T.151 Ligands: HH9.6 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:K.47, A:L.49, A:T.138, A:A.140, C:L.49, C:A.140 Halogen bonds: A:T.151 Salt bridges: C:K.47 HH9.4: 11 residues within 4Å: Chain B: K.47, L.49, T.138, A.140, T.151, V.153 Chain D: K.47, L.49, A.140, T.151 Ligands: HH9.8 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: D:L.49, D:A.140, B:K.47, B:L.49, B:T.138 Salt bridges: D:K.47 Water bridges: B:T.138, B:T.138, B:T.138 Halogen bonds: B:T.151 HH9.6: 11 residues within 4Å: Chain A: K.47, L.49, A.140, T.151 Chain C: K.47, L.49, T.138, A.140, T.151, V.153 Ligands: HH9.2 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:L.49, A:A.140, C:K.47, C:L.49, C:T.138, C:A.140 Salt bridges: A:K.47 Halogen bonds: C:T.151 HH9.8: 11 residues within 4Å: Chain B: K.47, L.49, A.140, T.151 Chain D: K.47, L.49, T.138, A.140, T.151, V.153 Ligands: HH9.4 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:K.47, D:L.49, D:T.138, B:L.49, B:A.140 Water bridges: D:T.138, D:T.138, D:T.138 Halogen bonds: D:T.151 Salt bridges: B:K.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitakami, R. et al., Inhibitory activities of anthraquinone and xanthone derivatives against transthyretin amyloidogenesis. Bioorg.Med.Chem. (2021)

Release Date

2021-10-13

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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