SMTL ID : 3ng5.1

Crystal Structure of V30M transthyretin complexed with (-)-epigallocatechin gallate (EGCG)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

6 x KDH: (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate(Non-covalent)

KDH.1: 11 residues within 4Å: Chain A: D.18, V.20, R.21, Y.78, W.79, L.82, I.84 Chain D: V.20, I.84, S.85, Y.114 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:I.84, D:V.20, D:I.84 Hydrogen bonds: A:R.21, A:R.21, A:Y.78, D:S.85, D:S.85 Water bridges: A:P.24, A:Y.78, A:Y.78, D:Y.114 Salt bridges: A:R.21 pi-Cation interactions: A:R.21 KDH.2: 9 residues within 4Å: Chain A: H.31, V.32, F.33, W.41, P.43, F.44, A.45, S.46, E.72 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.31, A:F.33, A:F.33, A:P.43 Hydrogen bonds: A:F.44, A:A.45, A:S.46, A:S.46, A:E.72 Water bridges: A:S.46, A:E.72 KDH.4: 9 residues within 4Å: Chain B: H.31, V.32, F.33, W.41, P.43, F.44, A.45, S.46, E.72 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:H.31, B:F.33, B:F.33, B:P.43 Hydrogen bonds: B:V.32, B:W.41, B:F.44, B:A.45, B:A.45, B:A.45, B:S.46, B:E.72 Water bridges: B:W.41, B:S.46, B:H.90 KDH.5: 11 residues within 4Å: Chain B: V.20, I.84, S.85, Y.114 Chain C: D.18, V.20, R.21, Y.78, W.79, L.82, I.84 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:V.20, B:I.84, C:I.84 Hydrogen bonds: B:S.85, B:S.85, C:R.21, C:R.21, C:Y.78 Water bridges: B:Y.114, C:P.24, C:Y.78, C:Y.78 Salt bridges: C:R.21 pi-Cation interactions: C:R.21 KDH.6: 9 residues within 4Å: Chain C: H.31, V.32, F.33, W.41, P.43, F.44, A.45, S.46, E.72 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:H.31, C:F.33, C:F.33, C:P.43 Hydrogen bonds: C:F.44, C:A.45, C:S.46, C:S.46, C:E.72 Water bridges: C:S.46, C:E.72 KDH.8: 9 residues within 4Å: Chain D: H.31, V.32, F.33, W.41, P.43, F.44, A.45, S.46, E.72 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:H.31, D:F.33, D:F.33, D:P.43 Hydrogen bonds: D:V.32, D:W.41, D:F.44, D:A.45, D:A.45, D:A.45, D:S.46, D:E.72 Water bridges: D:W.41, D:S.46, D:H.90

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: A.108, L.110, S.117, T.118, T.119 Chain C: L.17, L.110 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.117, A:T.119 GOL.7: 8 residues within 4Å: Chain A: L.17, L.110 Chain C: A.108, L.110, S.117, T.118, T.119 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.117, C:T.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyata, M. et al., Crystal structure of green tea polyphenol(-)-epigallocatechin gallate (EGCG)-transthyretin complex reveals novel binding site distinct from thyroxine binding site. Biochemistry (2010)

Release Date

2010-07-07

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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