SMTL ID : 3grb.1

Crystal structure of the F87M/L110M mutant of human transthyretin at pH 6.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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.1, H2O.3 ZN.2: 3 residues within 4Å: Chain A: H.88, H.90, E.92 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.88, A:H.90, A:E.92, H2O.3 ZN.6: 4 residues within 4Å: Chain A: H.31, E.72, D.74, H.90 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.31, A:E.72, A:D.74, H2O.3 ZN.7: 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.8: 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.6 ZN.9: 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.3 ZN.12: 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.6, H2O.9 ZN.13: 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.9 ZN.17: 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.9 ZN.19: 2 residues within 4Å: Chain D: C.10, H.56 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:C.10, D:H.56, H2O.11, H2O.11 ZN.20: 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.9 ZN.24: 3 residues within 4Å: Chain D: H.31, E.72, H.90 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.31, D:E.72, H2O.11

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.34, A.36, A.37 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.34, A:R.34, A:A.37 Water bridges: A:D.38, A:D.38 GOL.4: 13 residues within 4Å: Chain A: 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 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:M.110, C:S.117, A:L.111, A:S.117 GOL.5: 6 residues within 4Å: Chain A: W.41, K.70, E.92 Chain B: W.41, K.70, V.94 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.70, B:K.70 Water bridges: A:K.70 GOL.10: 4 residues within 4Å: Chain B: V.30, H.31, S.46, G.47 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.30, B:G.47 GOL.16: 6 residues within 4Å: Chain C: W.41, K.70, E.92 Chain D: W.41, K.70, V.94 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:W.41, D:K.70, C:K.70 Water bridges: D:E.92, C:K.70 GOL.18: 3 residues within 4Å: Chain C: R.34, A.36, A.37 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.34, C:R.34, C:A.37 GOL.23: 4 residues within 4Å: Chain D: H.31, S.46, G.47, K.48 No protein-ligand interaction detected (PLIP)

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

ACT.11: 8 residues within 4Å: Chain B: T.75, M.87, H.88, H.90, A.91, S.112, S.115, Y.116 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.91, B:Y.116 ACT.14: 9 residues within 4Å: Chain C: T.75, M.87, H.88, H.90, A.91, S.112, P.113, S.115, Y.116 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.112 ACT.15: 4 residues within 4Å: Chain C: G.57, L.58, T.59, E.63 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.63 ACT.21: 7 residues within 4Å: Chain C: P.86, M.87, Y.114 Chain D: T.96, D.99, Y.105, V.122 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.114, D:V.122 Water bridges: C:Y.114 Hydrogen bonds: D:Y.105 ACT.22: 8 residues within 4Å: Chain D: T.75, M.87, H.88, H.90, A.91, S.112, S.115, Y.116 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.91, D:Y.116 Hydrogen bonds: D:H.88 ACT.25: 8 residues within 4Å: Chain B: M.110, S.115, Y.116, S.117 Chain D: M.110, S.115, Y.116, S.117 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:M.110 Hydrogen bonds: D:S.117

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
D

D
C

Transthyretin

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