SMTL ID : 5k1j.1

Human TTR altered by a rhenium tris-carbonyl Pyta-C8 derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-tetramer

Ligands

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 3 residues within 4Å: Chain A: W.32, K.61, E.63 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.63 pi-Cation interactions: A:F.24 DMS.7: 9 residues within 4Å: Chain B: V.5, V.62, I.64, A.82, V.84, I.98, A.100, Y.107, T.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.107 DMS.12: 3 residues within 4Å: Chain C: W.32, K.61, E.63 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:E.63 pi-Cation interactions: C:F.24 DMS.18: 9 residues within 4Å: Chain D: V.5, V.62, I.64, A.82, V.84, I.98, A.100, Y.107, T.109 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.107

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

EDO.2: 7 residues within 4Å: Chain A: F.55, V.56, E.57, A.88, N.89, D.90, Y.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.90, A:D.90 EDO.8: 5 residues within 4Å: Chain B: F.24, W.32, K.61, E.63, E.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.61, B:E.83 EDO.9: 5 residues within 4Å: Chain A: H.81, E.83 Chain B: W.32, K.61, V.85 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.61, B:K.61, A:H.81 Water bridges: B:K.26, B:K.26 EDO.13: 7 residues within 4Å: Chain C: F.55, V.56, E.57, A.88, N.89, D.90, Y.96 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.90, C:D.90 EDO.19: 5 residues within 4Å: Chain D: F.24, W.32, K.61, E.63, E.83 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.61, D:E.83 EDO.20: 5 residues within 4Å: Chain C: H.81, E.83 Chain D: W.32, K.61, V.85 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.61, D:K.61, C:H.81 Water bridges: D:K.26, D:K.26

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: I.17, N.18, S.68, Y.69 4 PLIP interactions: 4 interactions with chain A Water bridges: A:A.20, A:K.39, A:Y.69 Salt bridges: A:K.39 ACT.4: 9 residues within 4Å: Chain A: V.84, V.85, F.86, T.109, T.110, A.111 Chain B: H.79, Y.105, S.106 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.79 Hydrophobic interactions: A:V.84 ACT.5: 4 residues within 4Å: Chain A: F.35, L.49, T.50, E.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.49 ACT.14: 4 residues within 4Å: Chain C: I.17, N.18, S.68, Y.69 4 PLIP interactions: 4 interactions with chain C Water bridges: C:A.20, C:K.39, C:Y.69 Salt bridges: C:K.39 ACT.15: 9 residues within 4Å: Chain C: V.84, V.85, F.86, T.109, T.110, A.111 Chain D: H.79, Y.105, S.106 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.84 Salt bridges: D:H.79 ACT.16: 4 residues within 4Å: Chain C: F.35, L.49, T.50, E.54 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.49

4 x RE: RHENIUM(Non-covalent)

RE.6: 2 residues within 4Å: Chain A: T.87 Chain B: H.79 Ligand excluded by PLIP RE.10: 2 residues within 4Å: Chain B: T.66, W.70 Ligand excluded by PLIP RE.17: 2 residues within 4Å: Chain C: T.87 Chain D: H.79 Ligand excluded by PLIP RE.21: 2 residues within 4Å: Chain D: T.66, W.70 Ligand excluded by PLIP

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.11: 4 residues within 4Å: Chain B: N.18, K.39, T.40, S.41 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.39 Water bridges: B:E.42 IMD.22: 4 residues within 4Å: Chain D: N.18, K.39, T.40, S.41 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.39 Water bridges: D:E.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ciccone, L. et al., Human TTR conformation altered by rhenium tris-carbonyl derivatives. J.Struct.Biol. (2016)

Release Date

2016-07-20

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