SMTL ID : 3dgd.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-tetramer

Ligands

15 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: H.31, D.74 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.74, A:D.74, H2O.5 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.4, H2O.4 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.4, H2O.4 ZN.6: 1 residues within 4Å: Chain A: E.61 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.61, A:E.61, H2O.5 ZN.7: 2 residues within 4Å: Chain B: C.10, H.56 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.10, H2O.8, H2O.8 ZN.8: 2 residues within 4Å: Chain B: H.31, D.74 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.74, H2O.8 ZN.9: 2 residues within 4Å: Chain B: H.88, H.90 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.88, B:H.90, H2O.8 ZN.13: 1 residues within 4Å: Chain B: E.62 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.62, B:E.62, H2O.8 ZN.16: 3 residues within 4Å: Chain C: H.88, H.90, E.92 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.88, C:H.90, C:E.92, H2O.8 ZN.17: 2 residues within 4Å: Chain C: C.10, H.56 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:C.10, C:H.56, H2O.11, H2O.12 ZN.22: 2 residues within 4Å: Chain C: H.31, D.74 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.31, C:D.74, C:D.74, H2O.12 ZN.23: 3 residues within 4Å: Chain D: H.31, D.74 Ligands: GOL.30 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.31, D:D.74, H2O.15 ZN.24: 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.12, H2O.15 ZN.25: 1 residues within 4Å: Chain D: E.62 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.62, D:E.62, H2O.14 ZN.26: 3 residues within 4Å: Chain D: H.88, H.90, E.92 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.88, D:H.90, D:E.92, H2O.12, H2O.15

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

ACT.4: 7 residues within 4Å: Chain A: W.41, K.70, E.92, V.94 Chain B: W.41, K.70, V.94 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.70, A:V.94 Water bridges: A:K.70, B:K.70 Salt bridges: A:K.70, B:K.70 ACT.5: 10 residues within 4Å: Chain A: T.75, W.79, P.86, M.87, H.88, H.90, A.91, S.112, P.113, Y.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.75 ACT.10: 5 residues within 4Å: Chain B: A.29, V.30, H.31, S.46, G.47 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.29 Hydrogen bonds: B:S.46, B:S.46 Water bridges: B:H.31, B:H.31, B:H.31 Salt bridges: B:H.31 ACT.11: 10 residues within 4Å: Chain B: T.75, W.79, P.86, M.87, H.88, H.90, A.91, S.112, P.113, Y.116 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.91, B:Y.116 Hydrogen bonds: B:T.75, B:S.112 ACT.12: 6 residues within 4Å: Chain B: H.31, V.32, P.43, F.44, A.45, S.46 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.32, B:F.44, B:A.45 ACT.18: 9 residues within 4Å: Chain C: T.75, W.79, P.86, M.87, H.88, H.90, A.91, S.112, P.113 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.75 ACT.19: 7 residues within 4Å: Chain C: P.86, M.87, Y.114 Chain D: T.96, D.99, Y.105, V.122 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.105, D:V.122, C:Y.114 ACT.20: 5 residues within 4Å: Chain C: G.57, L.58, T.59, T.60, E.63 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.57 Water bridges: C:T.59 ACT.21: 7 residues within 4Å: Chain C: W.41, K.70, V.94 Chain D: W.41, K.70, V.94 Ligands: ACT.29 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:K.70, C:W.41 Salt bridges: D:K.70, C:K.70 Water bridges: C:K.70 ACT.27: 9 residues within 4Å: Chain D: T.75, W.79, P.86, M.87, H.88, H.90, S.112, P.113, Y.116 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.116 Hydrogen bonds: D:S.112 ACT.28: 6 residues within 4Å: Chain D: H.31, V.32, P.43, F.44, A.45, S.46 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:P.43 Hydrogen bonds: D:V.32, D:F.44, D:A.45, D:S.46, D:S.46 Salt bridges: D:H.31 ACT.29: 5 residues within 4Å: Chain D: F.33, W.41, K.70, E.72 Ligands: ACT.21 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.41 Water bridges: D:W.41, D:K.70 Salt bridges: D:K.70

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 4 residues within 4Å: Chain B: E.42, P.43, F.44, E.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.43, B:E.63, B:E.63 GOL.15: 5 residues within 4Å: Chain A: D.39 Chain B: F.33, W.41, K.70, E.72 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.70, B:E.72 Water bridges: B:W.41, B:W.41, B:K.70, A:D.39 GOL.30: 5 residues within 4Å: Chain D: A.29, H.31, S.46, G.47 Ligands: ZN.23 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.47, D:G.47

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

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