SMTL ID : 3gps.1

Crystal structure of the F87M/L110M mutant of human transthyretin at pH 5.5

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: 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.2, H2O.2 ZN.2: 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.2, H2O.4 ZN.3: 4 residues within 4Å: Chain A: H.31, E.72, D.74, H.90 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.31, A:D.74, H2O.2 ZN.6: 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.3, H2O.4 ZN.7: 3 residues within 4Å: Chain B: H.31, E.72, D.74 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.31, B:E.72, B:D.74, H2O.3 ZN.8: 3 residues within 4Å: Chain B: H.88, H.90, E.92 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.88, B:H.90, B:E.92, H2O.4 ZN.15: 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.4, H2O.6 ZN.16: 3 residues within 4Å: Chain C: H.31, E.72, D.74 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.31, C:E.72, C:D.74, H2O.6 ZN.17: 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.5 ZN.22: 2 residues within 4Å: Chain D: C.10, H.56 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.10, D:H.56, H2O.7 ZN.23: 2 residues within 4Å: Chain D: H.31, D.74 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.31, D:D.74, D:D.74, H2O.8 ZN.24: 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.6, H2O.8

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

ACT.4: 7 residues within 4Å: Chain A: T.75, M.87, H.90, A.91, S.112, S.115, Y.116 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.75, A:A.91 Hydrogen bonds: A:S.112 ACT.9: 7 residues within 4Å: Chain A: W.41, K.70, E.92, V.94 Chain B: W.41, K.70 Ligands: GOL.13 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.94, B:K.70 Water bridges: A:K.70 Salt bridges: A:K.70, B:K.70 ACT.10: 11 residues within 4Å: Chain B: T.75, W.79, P.86, M.87, H.88, H.90, A.91, S.112, P.113, S.115, Y.116 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.91, B:Y.116 Hydrogen bonds: B:H.90 ACT.11: 4 residues within 4Å: Chain B: H.31, S.46, G.47, K.48 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.31, B:K.48 ACT.18: 4 residues within 4Å: Chain C: W.41, K.70 Chain D: W.41, K.70 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:W.41, C:K.70 Salt bridges: D:K.70, C:K.70 Hydrogen bonds: C:W.41 ACT.19: 11 residues within 4Å: Chain C: T.75, W.79, P.86, M.87, H.88, H.90, A.91, S.112, P.113, S.115, Y.116 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.86 Hydrogen bonds: C:H.88 ACT.20: 6 residues within 4Å: Chain C: H.31, V.32, P.43, F.44, A.45, S.46 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:P.43 Hydrogen bonds: C:V.32, C:F.44 Salt bridges: C:H.31 ACT.25: 9 residues within 4Å: Chain D: T.75, P.86, M.87, H.88, H.90, A.91, S.112, P.113, Y.116 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.86 Hydrogen bonds: D:S.112 Water bridges: D:T.75, D:T.75 ACT.26: 7 residues within 4Å: Chain C: T.96, D.99, Y.105, V.122 Chain D: P.86, M.87, Y.114 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.114, C:V.122 Hydrogen bonds: C:Y.105 ACT.27: 8 residues within 4Å: Chain A: A.19, M.110, L.111, S.112, S.115, Y.116, S.117 Chain D: S.115 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.19, A:M.110 Hydrogen bonds: A:S.112, A:S.117

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.34, A.36, A.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.34, A:R.34, A:A.37 GOL.12: 4 residues within 4Å: Chain B: E.42, P.43, F.44, E.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.43, B:E.63 GOL.13: 7 residues within 4Å: Chain A: K.35, D.39, W.41 Chain B: F.33, W.41, K.70 Ligands: ACT.9 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.39, A:W.41, B:K.70 Water bridges: A:D.39, B:T.40, B:E.72 GOL.14: 14 residues within 4Å: Chain B: A.19, M.110, L.111, S.112, S.115, Y.116, S.117 Chain C: A.19, M.110, L.111, S.112, S.115, Y.116, S.117 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.110, C:S.117, C:S.117 GOL.21: 3 residues within 4Å: Chain C: H.31, S.46, G.47 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.46, C:G.47 GOL.28: 3 residues within 4Å: Chain D: R.34, A.36, A.37 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.34, D:R.34, D:A.37 GOL.29: 4 residues within 4Å: Chain C: D.39, T.40 Chain D: T.40, W.41 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:W.41, D:W.41 Water bridges: C:W.41

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

2010-04-07

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Transthyretin

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