SMTL ID : 4n86.1

Crystal structure of human transthyretin complexed with glabridin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x GBJ: 4-[(3R)-8,8-dimethyl-3,4-dihydro-2H,8H-pyrano[2,3-f]chromen-3-yl]benzene-1,3-diol(Non-covalent)

GBJ.1: 13 residues within 4Å: Chain A: K.47, L.49, E.86, A.140, L.142, S.149 Chain C: K.47, L.49, A.140, A.141, L.142, S.149 Ligands: GBJ.4 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:K.47, A:L.142, A:L.142, C:K.47, C:K.47, C:L.49, C:A.140, C:L.142 Hydrogen bonds: A:K.47 GBJ.3: 12 residues within 4Å: Chain B: K.47, L.49, A.140, A.141, L.142, S.149 Chain D: K.47, L.49, A.140, L.142, S.149 Ligands: GBJ.6 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:K.47, B:K.47, B:L.49, B:A.140, B:L.142, D:L.142, D:L.142 Hydrogen bonds: B:S.149, D:K.47 GBJ.4: 13 residues within 4Å: Chain A: K.47, L.49, A.140, A.141, L.142, S.149 Chain C: K.47, L.49, E.86, A.140, L.142, S.149 Ligands: GBJ.1 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:K.47, A:K.47, A:L.49, A:A.140, A:L.142, C:K.47, C:L.142, C:L.142 Hydrogen bonds: C:K.47 GBJ.6: 12 residues within 4Å: Chain B: K.47, L.49, A.140, L.142, S.149 Chain D: K.47, L.49, A.140, A.141, L.142, S.149 Ligands: GBJ.3 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:K.47, D:K.47, D:L.49, D:A.140, D:L.142, B:L.142, B:L.142 Hydrogen bonds: D:S.149, B:K.47

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokoyama, T. et al., Crystal structures of human transthyretin complexed with glabridin. J.Med.Chem. (2014)

Release Date

2014-02-19

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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