SMTL ID : 3grg.1

Crystal structure of the F87M/L110M mutant of human transthyretin at pH 7.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.10, A:H.56 ZN.2: 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.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.2, H2O.3 ZN.7: 2 residues within 4Å: Chain B: C.10, H.56 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.10, B:H.56, H2O.5 ZN.8: 3 residues within 4Å: Chain B: H.31, E.72, D.74 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.31, B:E.72, B:D.74, B:D.74, H2O.3 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 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.10, C:H.56, H2O.6 ZN.13: 2 residues within 4Å: Chain C: H.31, D.74 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.31, C:D.74, C:D.74, H2O.6, H2O.7 ZN.14: 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.6 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.8, H2O.8 ZN.20: 3 residues within 4Å: Chain D: H.31, E.72, D.74 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.31, D:E.72, D:D.74, D:D.74, H2O.7 ZN.21: 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.7

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

ACT.4: 5 residues within 4Å: Chain A: W.41, K.70, E.92 Chain B: W.41, K.70 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.70 Water bridges: A:K.35, A:K.70 Salt bridges: A:K.70, B:K.70 ACT.6: 3 residues within 4Å: Chain A: R.34, A.36, A.37 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.37 Hydrogen bonds: A:A.37 Salt bridges: A:R.34 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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.91, B:Y.116 Hydrogen bonds: B:H.88, B:S.112 ACT.15: 10 residues within 4Å: Chain C: T.75, 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:S.112 ACT.16: 5 residues within 4Å: Chain C: W.41, K.70, V.94 Chain D: W.41, K.70 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.41 Water bridges: C:K.70 Salt bridges: C:K.70, D:K.70 ACT.22: 6 residues within 4Å: Chain C: P.86, M.87, Y.114 Chain D: T.96, Y.105, V.122 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.105, D:V.122, C:Y.114 Hydrogen bonds: D:Y.105, C:Y.114 Water bridges: D:D.99, C:Y.114 ACT.23: 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 12 residues within 4Å: Chain A: T.75, W.79, P.86, M.87, H.88, H.90, A.91, L.111, S.112, P.113, S.115, Y.116 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.75, A:H.90, A:S.112, A:S.112, A:S.115 GOL.11: 12 residues within 4Å: Chain B: A.19, M.110, L.111, S.112, S.115, Y.116, S.117 Chain D: A.19, M.110, S.112, S.115, S.117 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:S.112, D:M.110, D:S.117, D:S.117 GOL.17: 14 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, S.117 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:M.110, A:S.117, C:M.110, C:S.117 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:A.37 Water bridges: C:D.38

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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