SMTL ID : 4y9b.1

Crystal structure of V30M mutated transthyretin in complex with alpha-mangostin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x MKS: 1,3,6-trihydroxy-7-methoxy-2,8-bis(3-methylbut-2-en-1-yl)-9H-xanthen-9-one(Non-covalent)

MKS.1: 18 residues within 4Å: Chain A: K.47, T.138, A.140, L.142, S.149, T.150, T.151, V.153 Chain C: K.47, L.49, P.56, S.84, A.140, L.142, T.151 Ligands: CL.2, MKS.6, CL.7 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:T.138, A:A.140, A:V.153, A:V.153, C:K.47, C:P.56, C:L.142 Hydrogen bonds: C:K.47 Water bridges: C:T.151 MKS.4: 18 residues within 4Å: Chain B: K.47, L.49, P.56, S.84, A.140, L.142, T.151 Chain D: K.47, L.49, T.138, A.140, L.142, S.149, T.151, V.153 Ligands: CL.5, MKS.9, CL.10 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:L.49, D:T.138, D:A.140, D:L.142, D:V.153, D:V.153, B:K.47, B:L.49, B:P.56, B:L.142 Hydrogen bonds: B:K.47, B:T.151 MKS.6: 18 residues within 4Å: Chain A: K.47, L.49, P.56, S.84, A.140, L.142, T.151 Chain C: K.47, T.138, A.140, L.142, S.149, T.150, T.151, V.153 Ligands: MKS.1, CL.2, CL.7 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:K.47, A:P.56, A:L.142, C:T.138, C:A.140, C:V.153, C:V.153 Hydrogen bonds: A:K.47 Water bridges: A:T.151 MKS.9: 18 residues within 4Å: Chain B: K.47, L.49, T.138, A.140, L.142, S.149, T.151, V.153 Chain D: K.47, L.49, P.56, S.84, A.140, L.142, T.151 Ligands: MKS.4, CL.5, CL.10 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:K.47, D:L.49, D:P.56, D:L.142, B:L.49, B:T.138, B:A.140, B:L.142, B:V.153, B:V.153 Hydrogen bonds: D:K.47, D:T.151

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: K.47 Chain C: T.138, V.153 Ligands: MKS.1, MKS.6 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: T.138 Chain D: K.47 Ligands: MKS.4, MKS.9 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: T.138, V.153 Chain C: K.47 Ligands: MKS.1, MKS.6 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: K.47 Chain D: T.138 Ligands: MKS.4, MKS.9 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 1 residues within 4Å: Chain A: E.104 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.104, H2O.1 CA.8: 1 residues within 4Å: Chain C: E.104 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.104, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokoyama, T. et al., Discovery of gamma-Mangostin as an Amyloidogenesis Inhibitor. Sci Rep (2015)

Release Date

2015-09-09

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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