SMTL ID : 5k1n.1

Human TTR altered by a rhenium tris-carbonyl Pyta-C12 derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: A.27, E.33 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.25, A:R.25 EDO.2: 4 residues within 4Å: Chain A: F.35, L.49, T.50, E.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.49 Water bridges: A:T.51 EDO.10: 2 residues within 4Å: Chain C: A.27, E.33 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.25, C:R.25 EDO.11: 4 residues within 4Å: Chain C: F.35, L.49, T.50, E.54 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.49 Water bridges: C:T.51

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 7 residues within 4Å: Chain A: K.67, P.77, F.78, H.79, E.80 Chain B: I.59, T.87 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.67 Water bridges: A:E.80, B:T.87 PEG.12: 7 residues within 4Å: Chain C: K.67, P.77, F.78, H.79, E.80 Chain D: I.59, T.87 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:T.87, C:E.80 Hydrogen bonds: C:K.67

6 x RE: RHENIUM(Non-covalent)

RE.4: 5 residues within 4Å: Chain A: H.79, E.80, H.81 Chain B: V.84, V.85 Ligand excluded by PLIP RE.7: 3 residues within 4Å: Chain A: T.87 Chain B: H.79, Y.105 Ligand excluded by PLIP RE.8: 1 residues within 4Å: Chain B: Y.107 Ligand excluded by PLIP RE.13: 5 residues within 4Å: Chain C: H.79, E.80, H.81 Chain D: V.84, V.85 Ligand excluded by PLIP RE.16: 3 residues within 4Å: Chain C: T.87 Chain D: H.79, Y.105 Ligand excluded by PLIP RE.17: 1 residues within 4Å: Chain D: Y.107 Ligand excluded by PLIP

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

ACT.5: 6 residues within 4Å: Chain A: I.17, N.18, V.19, K.39, S.68, Y.69 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.18 Water bridges: A:A.20 Salt bridges: A:K.39 ACT.14: 6 residues within 4Å: Chain C: I.17, N.18, V.19, K.39, S.68, Y.69 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.18 Water bridges: C:A.20 Salt bridges: C:K.39

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

DMS.6: 4 residues within 4Å: Chain B: F.35, L.49, T.50, E.54 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.50, B:T.51 pi-Cation interactions: B:F.35 DMS.15: 4 residues within 4Å: Chain D: F.35, L.49, T.50, E.54 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.50, D:T.51 pi-Cation interactions: D:F.35

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.9: 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:N.18 Water bridges: B:E.42 IMD.18: 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:N.18 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

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