SMTL ID : 4y9f.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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: 20 residues within 4Å: Chain A: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151, V.153 Chain C: K.47, L.49, P.56, A.140, L.142, S.149, T.151 Ligands: BR.2, MKT.11, BR.12, BR.13 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:L.49, A:T.138, A:A.140, A:L.142, A:T.151, A:V.153, A:V.153, C:K.47, C:L.49, C:P.56, C:A.140, C:L.142 Hydrogen bonds: C:K.47 MKT.7: 23 residues within 4Å: Chain B: K.47, L.49, P.56, S.84, A.140, L.142, S.149, 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: BR.8, BR.9, MKT.17, BR.18, BR.19 13 PLIP interactions: 7 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:L.49, D:T.138, D:A.140, D:L.142, D:T.151, D:V.153, D:V.153, B:K.47, B:L.49, B:L.49, B:P.56, B:A.140, B:L.142 MKT.11: 20 residues within 4Å: Chain A: K.47, L.49, P.56, A.140, L.142, S.149, T.151 Chain C: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151, V.153 Ligands: MKT.1, BR.2, BR.3, BR.12 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:L.49, C:T.138, C:A.140, C:L.142, C:T.151, C:V.153, C:V.153, A:K.47, A:L.49, A:P.56, A:A.140, A:L.142 Hydrogen bonds: A:K.47 MKT.17: 23 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, S.84, A.140, L.142, S.149, T.151, V.153 Ligands: MKT.7, BR.8, BR.9, BR.18, BR.19 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:L.142, B:T.151, B:V.153, B:V.153, D:K.47, D:L.49, D:L.49, D:P.56, D:A.140, D:L.142

16 x BR: BROMIDE ION(Non-covalent)

BR.2: 7 residues within 4Å: Chain C: A.140, L.142, S.149, T.150, T.151 Ligands: MKT.1, MKT.11 Ligand excluded by PLIP BR.3: 3 residues within 4Å: Chain C: T.138, V.153 Ligands: MKT.11 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: 2 residues within 4Å: Chain A: K.67 Chain B: H.122 Ligand excluded by PLIP BR.8: 3 residues within 4Å: Chain D: K.47 Ligands: MKT.7, MKT.17 Ligand excluded by PLIP BR.9: 7 residues within 4Å: Chain B: A.140, L.142, S.149, T.150, T.151 Ligands: MKT.7, MKT.17 Ligand excluded by PLIP BR.10: 4 residues within 4Å: Chain A: H.122 Chain B: K.67, I.100, V.126 Ligand excluded by PLIP BR.12: 7 residues within 4Å: Chain A: A.140, L.142, S.149, T.150, T.151 Ligands: MKT.1, MKT.11 Ligand excluded by PLIP BR.13: 3 residues within 4Å: Chain A: T.138, V.153 Ligands: MKT.1 Ligand excluded by PLIP BR.14: 1 residues within 4Å: Chain C: H.63 Ligand excluded by PLIP BR.15: 2 residues within 4Å: Chain C: S.82, E.83 Ligand excluded by PLIP BR.16: 2 residues within 4Å: Chain C: K.67 Chain D: H.122 Ligand excluded by PLIP BR.18: 3 residues within 4Å: Chain B: K.47 Ligands: MKT.7, MKT.17 Ligand excluded by PLIP BR.19: 7 residues within 4Å: Chain D: A.140, L.142, S.149, T.150, T.151 Ligands: MKT.7, MKT.17 Ligand excluded by PLIP BR.20: 4 residues within 4Å: Chain C: H.122 Chain D: K.67, I.100, V.126 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

Related Entries With Identical Sequence