SMTL ID : 4y9c.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 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: 17 residues within 4Å: Chain A: L.49, 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: MKS.9, BR.10 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:K.47, C:L.49, C:P.56, C:L.142, A:L.49, A:T.138, A:A.140, A:T.151, A:V.153, A:V.153 Hydrogen bonds: C:K.47 MKS.7: 21 residues within 4Å: Chain B: K.47, L.49, P.56, S.84, A.140, L.142, S.149, T.151 Chain D: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151, V.153, T.155 Ligands: BR.8, MKS.15, BR.16 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:K.47, B:L.49, B:P.56, B:A.140, B:L.142, D:L.49, D:T.138, D:A.140, D:T.151, D:V.153, D:V.153, D:T.155 Water bridges: B:T.151 MKS.9: 17 residues within 4Å: Chain A: K.47, L.49, P.56, S.84, A.140, L.142, T.151 Chain C: L.49, T.138, A.140, L.142, S.149, T.150, T.151, V.153 Ligands: MKS.1, BR.2 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:L.49, C:T.138, C:A.140, C:T.151, C:V.153, C:V.153, A:K.47, A:L.49, A:P.56, A:L.142 Hydrogen bonds: A:K.47 MKS.15: 21 residues within 4Å: Chain B: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151, V.153, T.155 Chain D: K.47, L.49, P.56, S.84, A.140, L.142, S.149, T.151 Ligands: MKS.7, BR.8, BR.16 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:L.49, B:T.138, B:A.140, B:T.151, B:V.153, B:V.153, B:T.155, D:K.47, D:L.49, D:P.56, D:A.140, D:L.142 Water bridges: D:T.151

12 x BR: BROMIDE ION(Non-covalent)

BR.2: 4 residues within 4Å: Chain A: K.47 Chain C: T.138, V.153 Ligands: MKS.9 Ligand excluded by PLIP BR.3: 4 residues within 4Å: Chain A: K.67, W.73, I.100 Chain B: H.122 Ligand excluded by PLIP BR.4: 1 residues within 4Å: Chain A: H.63 Ligand excluded by PLIP BR.5: 2 residues within 4Å: Chain A: S.82, E.83 Ligand excluded by PLIP BR.6: 3 residues within 4Å: Chain A: H.122 Chain B: K.67, I.100 Ligand excluded by PLIP BR.8: 3 residues within 4Å: Chain D: K.47 Ligands: MKS.7, MKS.15 Ligand excluded by PLIP BR.10: 4 residues within 4Å: Chain A: T.138, V.153 Chain C: K.47 Ligands: MKS.1 Ligand excluded by PLIP BR.11: 4 residues within 4Å: Chain C: K.67, W.73, I.100 Chain D: H.122 Ligand excluded by PLIP BR.12: 1 residues within 4Å: Chain C: H.63 Ligand excluded by PLIP BR.13: 2 residues within 4Å: Chain C: S.82, E.83 Ligand excluded by PLIP BR.14: 3 residues within 4Å: Chain C: H.122 Chain D: K.67, I.100 Ligand excluded by PLIP BR.16: 3 residues within 4Å: Chain B: K.47 Ligands: MKS.7, MKS.15 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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