SMTL ID : 4deu.1

Crystal Structure of the Wild Type TTR Binding Naringenin (TTRwt:NAR)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 2 residues within 4Å: Chain A: F.36, A.37 Ligand excluded by PLIP EDO.2: 2 residues within 4Å: Chain A: E.58, D.91 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: V.114, T.115 Chain C: G.14, S.15, P.16 Ligands: EDO.4 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain C: P.16, I.18, E.43 Ligands: EDO.3 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: S.38, G.39 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: D.66, K.68, S.69, E.81 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: K.40, S.42, E.46, L.47, H.48 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain B: E.58, D.91 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain B: R.26, K.27, G.59, I.60 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: K.62, H.82, E.84 Chain B: W.33, K.62, E.84 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain C: F.36, A.37 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain C: E.58, D.91 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: G.14, S.15, P.16 Chain C: V.114, T.115 Ligands: EDO.17 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: P.16, I.18, E.43 Ligands: EDO.16 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain C: S.38, G.39 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain C: D.66, K.68, S.69, E.81 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain C: K.40, S.42, E.46, L.47, H.48 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain D: E.58, D.91 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain D: R.26, K.27, G.59, I.60 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain C: K.62, H.82, E.84 Chain D: W.33, K.62, E.84 Ligand excluded by PLIP

4 x NAR: NARINGENIN(Non-covalent)(Covalent)

NAR.5: 13 residues within 4Å: Chain A: K.7, L.9, A.100, S.109, T.110, T.111 Chain B: S.107 Chain C: K.7, L.9, A.100, L.102, V.113 Ligands: NAR.18 14 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: C:L.9, C:A.100, C:L.102, A:K.7, A:A.100 Hydrogen bonds: C:K.7, C:K.7, B:S.107 Water bridges: C:S.109, B:S.107, B:Y.108, A:S.109, A:S.109, A:S.109 NAR.10: 13 residues within 4Å: Chain B: K.7, A.100, L.102, S.109, V.113 Chain C: S.107 Chain D: K.7, L.9, A.100, S.109, T.110, T.111 Ligands: NAR.23 17 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: D:L.9, D:A.100, B:K.7, B:A.100, B:L.102 Hydrogen bonds: D:K.7, D:K.7, D:T.111, C:S.107, B:K.7 Water bridges: C:S.107, C:S.109, B:K.7, B:S.109, B:S.109, B:S.109, B:S.109 NAR.18: 13 residues within 4Å: Chain A: K.7, L.9, A.100, L.102, V.113 Chain C: K.7, L.9, A.100, S.109, T.110, T.111 Chain D: S.107 Ligands: NAR.5 14 PLIP interactions: 7 interactions with chain A, 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: A:L.9, A:A.100, A:L.102, C:K.7, C:A.100 Hydrogen bonds: A:K.7, A:K.7, D:S.107 Water bridges: A:S.109, A:S.109, C:S.109, C:S.109, D:S.107, D:Y.108 NAR.23: 13 residues within 4Å: Chain A: S.107 Chain B: K.7, L.9, A.100, S.109, T.110, T.111 Chain D: K.7, A.100, L.102, S.109, V.113 Ligands: NAR.10 17 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: B:L.9, B:A.100, D:K.7, D:A.100, D:L.102 Hydrogen bonds: B:K.7, B:K.7, B:T.111, A:S.107, D:K.7 Water bridges: A:S.107, A:S.109, A:S.109, A:S.109, D:K.7, D:S.109, D:S.109

2 x CA: CALCIUM ION(Non-covalent)

CA.11: 3 residues within 4Å: Chain B: E.58, N.90, P.94 No protein-ligand interaction detected (PLIP) CA.24: 3 residues within 4Å: Chain D: E.58, N.90, P.94 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trivella, D.B. et al., Flavonoid interactions with human transthyretin: Combined structural and thermodynamic analysis. J.Struct.Biol. (2012)

Release Date

2012-11-21

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin