SMTL ID : 3did.1

Crystal structure of the F87M/L110M mutant of human transthyretin at pH 4.6 soaked

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-tetramer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: H.31, D.74 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.31, A:D.74, A:D.74, H2O.2 ZN.2: 2 residues within 4Å: Chain A: C.10, H.56 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.10, A:H.56, H2O.1, H2O.3 ZN.3: 3 residues within 4Å: Chain A: H.88, H.90, E.92 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.88, A:H.90, A:E.92, H2O.3, H2O.3 ZN.8: 2 residues within 4Å: Chain B: C.10, H.56 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.10, B:H.56, H2O.6, H2O.6 ZN.9: 2 residues within 4Å: Chain B: H.31, D.74 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.74 ZN.10: 3 residues within 4Å: Chain B: H.88, H.90, E.92 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.88, B:H.90, B:E.92, H2O.5, H2O.6 ZN.12: 3 residues within 4Å: Chain C: H.88, H.90, E.92 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.88, C:H.90, C:E.92, H2O.8, H2O.9 ZN.13: 2 residues within 4Å: Chain C: H.31, D.74 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.74, C:D.74, H2O.7, H2O.8 ZN.14: 2 residues within 4Å: Chain C: C.10, H.56 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:C.10, H2O.6, H2O.8 ZN.16: 3 residues within 4Å: Chain D: H.31, E.72, D.74 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.31, D:E.72, D:D.74, H2O.11 ZN.17: 2 residues within 4Å: Chain D: C.10, H.56 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:C.10, H2O.9, H2O.12 ZN.18: 3 residues within 4Å: Chain D: H.88, H.90, E.92 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.88, D:H.90, D:E.92, H2O.11

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

ACT.4: 4 residues within 4Å: Chain A: W.41, K.70 Chain B: W.41, K.70 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.70 Water bridges: A:K.70 Salt bridges: A:K.70, B:K.70 ACT.5: 8 residues within 4Å: Chain A: T.75, W.79, P.86, M.87, H.88, S.112, P.113, Y.116 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.116 Hydrogen bonds: A:H.88, A:H.90 ACT.6: 2 residues within 4Å: Chain A: E.54, H.56 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.56 Salt bridges: A:H.56 ACT.15: 8 residues within 4Å: Chain C: T.75, M.87, H.88, H.90, A.91, S.112, P.113, Y.116 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.116 Hydrogen bonds: C:H.88 ACT.19: 10 residues within 4Å: Chain D: T.75, W.79, P.86, M.87, H.88, H.90, S.112, P.113, S.115, Y.116 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.75 ACT.20: 7 residues within 4Å: Chain C: P.86, M.87, Y.114 Chain D: T.96, N.98, Y.105, V.122 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.114

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: R.34, A.36, A.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.34, A:A.37 GOL.11: 4 residues within 4Å: Chain B: E.42, P.43, F.44, E.63 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.43, B:E.63, B:E.63, B:E.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palmieri, L.de.C. et al., Novel Zn2+-binding sites in human transthyretin: implications for amyloidogenesis and retinol-binding protein recognition. J.Biol.Chem. (2010)

Release Date

2008-07-22

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Transthyretin

Related Entries With Identical Sequence