SMTL ID : 4y9e.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-tetramer

Ligands

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

MKT.1: 19 residues within 4Å: Chain A: K.47, L.49, T.138, A.140, L.142, S.149, T.151, V.153 Chain C: K.47, L.49, P.56, S.84, A.140, L.142, T.151 Ligands: CL.2, MKT.7, CL.8, CL.9 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:K.47, A:L.49, A:T.138, A:A.140, A:L.142, A:L.142, A:V.153, A:V.153 Hydrogen bonds: C:K.47 MKT.4: 21 residues within 4Å: Chain B: K.47, L.49, P.56, A.140, L.142, T.151, V.153 Chain D: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151, V.153 Ligands: CL.5, CL.6, MKT.10, CL.11, CL.12 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:L.142, D:K.47, D:L.49, D:T.138, D:A.140, D:V.153, D:V.153 Hydrogen bonds: B:T.151 MKT.7: 19 residues within 4Å: Chain A: K.47, L.49, P.56, S.84, A.140, L.142, T.151 Chain C: K.47, L.49, T.138, A.140, L.142, S.149, T.151, V.153 Ligands: MKT.1, CL.2, CL.3, CL.8 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain C Hydrogen bonds: A:K.47 Hydrophobic interactions: C:K.47, C:L.49, C:T.138, C:A.140, C:L.142, C:L.142, C:V.153, C:V.153 MKT.10: 21 residues within 4Å: Chain B: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151, V.153 Chain D: K.47, L.49, P.56, A.140, L.142, T.151, V.153 Ligands: MKT.4, CL.5, CL.6, CL.11, CL.12 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:L.142, B:K.47, B:L.49, B:T.138, B:A.140, B:V.153, B:V.153 Hydrogen bonds: D:T.151

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

CL.2: 6 residues within 4Å: Chain C: A.140, S.149, T.150, T.151 Ligands: MKT.1, MKT.7 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: K.47 Chain C: V.153 Ligands: MKT.7 Ligand excluded by PLIP CL.5: 7 residues within 4Å: Chain B: A.140, L.142, S.149, T.150, T.151 Ligands: MKT.4, MKT.10 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain D: K.47 Ligands: MKT.4, MKT.10 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: A.140, S.149, T.150, T.151 Ligands: MKT.1, MKT.7 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: V.153 Chain C: K.47 Ligands: MKT.1 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain D: A.140, L.142, S.149, T.150, T.151 Ligands: MKT.4, MKT.10 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: K.47 Ligands: MKT.4, MKT.10 Ligand excluded by PLIP

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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